SECOND AMENDMENT AND ACCESSION AGREEMENT

Exhibit 10.38

Execution Version

SECOND AMENDMENT AND ACCESSION AGREEMENT

dated as of June 6, 2008

among

EQUINIX SINGAPORE PTE. LTD.,

EQUINIX JAPAN K.K.,

EQUINIX AUSTRALIA PTY LIMITED ABN 25 092 807 264,

EQUINIX HONG KONG LIMITED,

as Borrowers

ABN AMRO Bank N.V., Singapore Branch,

ABN AMRO Bank N.V., Japan Branch,

ABN AMRO Australia Pty Limited ABN 78 000 862 797,

Coöperatieve Centrale Raiffeisen-Boerenleenbank B.A., Hong Kong Branch,

as Lenders

and

ABN AMRO BANK N.V.,

as Facility Agent, Arranger and Collateral Agent

SECOND AMENDMENT AND ACCESSION AGREEMENT

This SECOND AMENDMENT AND ACCESSION AGREEMENT (this “ Amendment ”) dated as of June 6, 2008, among:

WITNESSETH:

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NOW, THEREFORE, the parties hereto agree as follows:

ARTICLE I

DEFINITIONS

SECTION 1.01 Defined Terms . Unless expressly defined in this Amendment, or the context otherwise requires, terms defined in the Amended Facility Agreement shall have the same meanings in this Amendment.

SECTION 1.02 Rules of Construction . The principles of construction and rules of interpretation set forth in Section 1.02 of the Amended Facility Agreement shall apply in this Amendment.

ARTICLE II

ACCESSION

SECTION 2.01 Accession . Each of the HK Dollar Lender and Equinix HK agrees with each other person who is or who becomes a party to the Amended Facility Agreement that, with effect on and from the date hereof, each of the HK Dollar Lender and Equinix HK will be bound by the Amended Facility Agreement as a party to the Amended Facility Agreement as of the date hereof in the capacity of “Lender”, with respect to the HK Dollar Lender, and “Borrower”, with respect to Equinix HK.

ARTICLE III

AMENDMENTS TO THE AMENDED FACILITY AGREEMENT

SECTION 3.01 New Definitions . The following new definitions are added to Section 1.01 (Defined Terms) of the Amended Facility Agreement in their proper alphabetical order:

“ Agency Fee ” shall have the meaning assigned to such term in Section 2.06(c) .

“ Equinix HK ” shall mean Equinix Hong Kong Limited, a company with limited liability incorporated under the laws of Hong Kong with its registered address at Suite 6208, 62/F Central Plaza, 18 Harbour Road, Wanchai, Hong Kong.

“ Facility Set-up Fees ” shall have the meaning assigned to such term in Section 2.06(b) .

“ HIBOR ” shall mean, with respect to any HK Dollar Borrowing for any Interest Period, the rate per annum for deposits in HK Dollars for a period equal to or that most closely approximates the duration of such Interest Period which appears on Reuters page “HIBOR=R”(or such other page(s) as may replace that page as determined by the Facility Agent) as of 11:00 a.m., Hong Kong time on the relevant Interest Rate Setting Date; provided that if such rate does not appear on that page, “HIBOR” shall mean the rate expressed as a percentage to be the arithmetic mean (rounded upwards, if necessary, to the nearest four decimal places) as supplied to the Facility Agent at its request quoted by at least two Reference Banks that are leading banks as the rate at which it is offered deposits in HK Dollars and for the required period in the Hong Kong interbank market at or about 11:00 a.m., Hong Kong time.

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“ HK Deed of Charge ” shall mean that certain Deed of Charge executed by the HK Dollar Borrower and the Collateral Agent dated as of June 6, 2008.

“ HK Dollar Borrower ” shall mean, in its capacity as the borrower of HK Dollar Loans, Equinix HK.

“ HK Dollar Borrowing ” shall mean a borrowing comprised of HK Dollar Loans made by the HK Dollar Lenders pursuant to a Borrowing Request.

“ HK Dollar Equivalent ” shall mean at any time (a) as to any amount denominated in HK Dollars, the amount thereof at such time, and (b) as to any amount denominated in any other currency, the equivalent amount in HK Dollars calculated by the Facility Agent at such time using the Exchange Rate in effect on the Business Day of determination.

“ HK Dollar Lender ” shall mean each financial institution listed on Schedule 1.01(e) (as amended from time to time), as well as any financial institution that has become a “HK Dollar Lender” hereto pursuant to Section 2.03 or by the execution of an Assignment and Assumption in accordance with this Agreement, other than, in each case, any such financial institution that has ceased to be a party hereto pursuant to an Assignment and Assumption. For purposes of this Agreement, “Lender” includes each HK Dollar Lender unless the context otherwise requires.

“ HK Dollar Loan Commitment ” shall mean, with respect to each Lender, the commitment, if any, of such Lender to make HK Dollar Loans hereunder during the Availability Period in the amount set forth opposite such Lender’s name on Schedule 1.01(e), or in the Assignment and Assumption pursuant to which such Lender shall have assumed its HK Dollar Loan Commitment, as applicable, as the same may be (a) increased pursuant to any Increased Commitment made by such Lender pursuant to Section 2.03 or (b) reduced or increased from time to time pursuant to assignments by or to such Lender pursuant to Section 10.04. The initial aggregate amount of the HK Dollar Loan Commitment is the HK Dollar Equivalent of US$20,000,000.

“ HK Dollar Loans ” shall mean the term loans made by the HK Dollar Lenders to the HK Dollar Borrower pursuant to Section 2.01(d).

“ HK Dollars ” or “ HKD ” shall mean the lawful currency of Hong Kong.

“ HK Share Charge ” shall mean that certain Share Charge executed by Equinix Pacific Inc. and the Collateral Agent dated as of June 6, 2008.

“ Hong Kong ” shall mean the Hong Kong Special Administrative Region of the People’s Republic of China.

SECTION 3.02 Deleted Definitions . The definitions of “ Amendment ” and “ Facility Set-up Fee ” as found in the Amended Facility Agreement are deleted.

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SECTION 3.03 Amended Definitions . The following definitions as found in the Amended Facility Agreement are deleted and replaced with the following in their proper alphabetical order:

“ Approved Currency ” shall mean, with respect to (i) the Singapore Dollar Borrower, Singapore Dollars, (ii) the Yen Borrower, Yen, (iii) the Australian Dollar Borrower, Australian Dollars and (iv) the HK Dollar Borrower, HK Dollars.

“ Availability Period ” shall mean the period commencing on the date that all conditions precedent to the making of the initial Loans under Section 4.01 and Section 4.02 have been satisfied or waived and ending, (i) on August 31, 2008 with respect to the Singapore Dollar Loans and the Yen Loans, (ii) on January 31, 2009 with respect to the Australian Dollar Loans, and (iii) on June 6, 2009 with respect to the HK Dollar Loans.

“ Borrowing ” shall mean a Singapore Dollar Borrowing, a Yen Borrowing, an Australian Dollar Borrowing or a HK Dollar Borrowing.

“ Collateral ” shall include (i) the “Collateral” as such term is defined and used in the Debenture, (ii) the “Movables” as such term is defined and used in the Assignment of Movables, (iii) the Secured Property as such term is defined and used in the Australia Deed of Charge and Australia Share Mortgage, and (iv) the Security Assets as such term is defined and used in the HK Deed of Charge and HK Share Charge.

“ Fees ” shall mean the Commitment Fee, the Facility Set-up Fees and the Agency Fee.

“ Final Maturity Date ” shall mean, with respect to (i) the Singapore Dollar Loans and the Yen Loans, August 31, 2011 or, if such date is not a Business Day, the Business Day immediately preceding such date, (ii) the Australian Dollar Loans, January 31, 2012 or, if such date is not a Business Day, the Business Day immediately preceding such date, and (iii) the HK Dollar Loans, June 6, 2012 or, if such date is not a Business Day, the Business Day immediately preceding such date.

“ GAAP ” shall mean generally accepted accounting principles in the United States applied on a consistent basis; provided that, at the option of the relevant Borrower, (i) GAAP shall mean generally accepted accounting principles in Singapore applied on a consistent basis, in relation to the annual financial reports to be delivered by the Singapore Dollar Borrower in accordance with this Agreement, (ii) GAAP shall mean generally accepted accounting principles in Japan applied on a consistent basis in relation to the annual financial reports to be delivered by the Yen Borrower in accordance with this Agreement, (iii) GAAP shall mean generally accepted accounting principles in Australia applied on a consistent basis in relation to the annual financial reports to be delivered by the Australian Dollar Borrower in accordance with this Agreement, and (iv) GAAP shall mean generally accepted accounting principles in Hong Kong applied on a consistent basis in relation to the annual financial reports to be delivered by the HK Dollar Borrower in accordance with this Agreement.

“ Interest Payment Date ” shall mean with respect to (i) the Singapore Dollar Loans and the Yen Loans, the last day of November, February, May and August of each year, from August 31, 2007 until the relevant Final Maturity Date, (ii) the Australian Dollar Loans, the last day of April, July, October and January of each year, from April 30, 2008 until the

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relevant Final Maturity Date, and (iii) the HK Dollar Loans, the last day of September, December, March and June of each year, from September 30, 2008; provided that if any Interest Payment Date shall fall on a day other than a Business Day, such Interest Payment Date shall be on the next preceding Business Day.

“ Interest Rate Setting Date ” shall mean two (2) Business Days before the start of any Interest Period, provided that in respect of any HK Dollar Loan, the Interest Rate Setting Date shall mean the first day of any Interest Period.

“ Material Indebtedness ” shall mean any Indebtedness (other than the Indebtedness under the Loan Documents) of any Borrower, any of their respective Subsidiaries or the Guarantor in an aggregate outstanding principal amount exceeding the US Dollar Equivalent of US$5,000,000.

“ Notes ” shall mean any notes evidencing the Singapore Dollar Loans, the Yen Loans, the Australian Dollar Loans or the HK Dollar Loans issued pursuant to this Agreement, if any, substantially in the form of Exhibits D-1 , D-2 , D-3 and D-4 .

“ Payment Office ” means (i) with respect to Singapore Dollar Borrowings, the Facility Agent’s office located at One Raffles Quay (ORQ) South Tower, Level 26, Singapore 048583, (ii) with respect to Yen Borrowings, the Facility Agent’s office located at Atago Green Hills Mori Tower 31F, 5-1 Atago 2-Chome, Minato-Ku, Tokyo, Japan, (iii) with respect to Australian Dollar Borrowings, the Facility Agent’s office located at Level 22, ABN AMRO Tower, 88 Philip Street, Sydney 2000 Australia, (iv) with respect to HK Dollar Borrowings, the Facility Agent’s office located at 38/F, Cheung Kong Center, 2 Queen’s Road Central, Hong Kong, or (v) at such other office or offices of the Facility Agent as may be designated in writing from time to time by the Facility Agent to Borrowers.

“ Reference Bank ” shall mean either (i) ABN AMRO Bank N.V. or (ii) Coöperatieve Centrale Raiffeisen-Boerenleenbank B.A., Hong Kong Branch.

“ Required Lenders ” shall mean (i) Lenders having more than 66 2/3% of the sum of all Loans outstanding and unused Loan Commitments, (ii) and at least two Lenders that are not Affiliates of another (if any).

“ Security Agreements ” shall mean the (i) Assignment of Movables, (ii) Debenture, (iii) Japan Share Pledge, (iv) Singapore Share Charge, (v) Australia Deed of Charge, (vi) Australia Share Mortgage, (vii) HK Deed of Charge and (viii) HK Share Charge.

“ Site Leases ” shall mean the lease by Equinix Japan over the following premises: (i) TRC-C Building, B-Block, 4th & 5th Floors & one-half of 1st floor, 1-1 Heiwajima, 6-chome, Oota-ku, Tokyo 143-0006 Japan and (ii) 8-21, Higashi-Shinagawa 3-chome, Shinagawa-ku, Tokyo, Shinshuu Meitetsu Shinagawa Building; the lease by Equinix Singapore over the following premises: (i) Blk 20 Ayer Rajah Crescent #06-01, #06-05/06/07/08, #05-05/06/06A/07/07A/08, #03-05/06/07/08 and #05-01/02/02A/03/03A/04 Singapore 139964, (ii) Blk 20 Ayer Rajah Crescent, #03-01 to #03-04, Singapore 139964, (iii) Blk 20 Ayer Rajah Crescent #04-05/06/06A/07/07A/08 Singapore 139964, (iv) Blk 20 Ayer Rajah Crescent #06-04 Singapore 139964, (v) Blk 20 Ayer Rajah Crescent #02-03/04 Singapore 139964, (vi) Blk 20 Ayer Rajah Crescent #06-02/03 Singapore 139964, (vii) Rooftop, Blk 20 Ayer Rajah Crescent Singapore 139964 and (viii) Cargo Lift Shafts G and H, Blk 20 Ayer Rajah Crescent Singapore 139964; the lease by Equinix Australia over the

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following premises: Units B, C1 and C2 and ancillary car parking spaces, 639 Gardeners Road, Mascot, New South Wales; and the lease and/or occupation license agreement by Equinix HK over the following premises: (i) Units 2 & 3, 13th floor, Global Gateway (Hong Kong), 168 Yeung Uk Road and 98 Wang Lung Street, Tsuen Wan, New Territories, Hong Kong; (ii) Units 1, 2 & 3, 17th floor, Global Gateway (Hong Kong), 168 Yeung Uk Road and 98 Wang Lung Street, Tsuen Wan, New Territories, Hong Kong; (iii) Units 1A, 1B & 2, 18th floor, Global Gateway (Hong Kong), 168 Yeung Uk Road and 98 Wang Lung Street, Tsuen Wan, New Territories, Hong Kong and (iv) those parts known as (1) switch room H on carpark level 2, (2) portions of common area for the installation of chilled water pipes from 13th floor to rook floor (inclusive), (3) portions of common area on roof floor for the installation of chiller plants and ancillary equipment, (4) portions of common area for the installation of two busbar risers and telco trunkings from carpark level 1 to 27th floor (inclusive), (5) portions of common area on 13th floor for the installation of pre-action valve(s) and (6) portions of common area for the installation of metal trunking from 13th floor to 17th floor (inclusive) of Global Gateway (Hong Kong), 168 Yeung Uk Road and 98 Wang Lung Street, Tsuen Wan, New Territories, Hong Kong.

SECTION 3.04 Commitments . Section 2.01 (Commitments) of the Amended Facility Agreement is amended by:

(a) deleting the word “and” at the end of Section 2.01(c); and

(b) adding a new Section 2.01(d) as follows:

“(d) each HK Dollar Lender agrees, severally and not jointly, to make HK Dollar Loans to the HK Dollar Borrower during the Availability Period in the principal amount not to exceed such HK Dollar Lender’s HK Dollar Loan Commitment; and”.

SECTION 3.05 Loans . Section 2.02(b) of the Amended Facility Agreement is amended by:

(a) deleting the word “and” before “(iii)”; and

(b) adding the following language after “Sydney time,”:

“and (iv) each HK Dollar Lender shall make each HK Dollar Loan to be made by it hereunder by wire transfer of immediately available funds to such account in Hong Kong as the Facility Agent may designate not later than 11:00 a.m., Hong Kong time,”.

SECTION 3.06 Borrowing Procedure . Section 2.04 (Borrowing Procedure) of the Amended Facility Agreement is amended by:

(a) deleting the word “or” before “(iii)”;

(b) adding the following language at the end of the second sentence of the first paragraph:

“or (iv) in the case of a HK Dollar Borrowing, not later than 11:00 a.m., Hong Kong time, three (3) Business Days before the date of the proposed Borrowing.”; and

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(c) deleting sub-paragraph (a) in its entirety and replacing it with the following:

“(a) whether the requested Borrowing is to be a Singapore Dollar Borrowing, a Yen Borrowing, an Australian Dollar Borrowing or a HK Dollar Borrowing; provided, however, that the Singapore Dollar Borrower, the Yen Borrower, the Australian Dollar Borrower and the HK Dollar Borrower may request only Singapore Dollar Borrowings, Yen Borrowings, Australian Dollar Borrowings and HK Dollar Borrowings, respectively;”.

SECTION 3.07 Promise to Repay . Section 2.05(a) (Promise to Repay) of the Amended Facility Agreement is amended by:

(a) deleting the word “and” before “(iii)”; and

(b) adding the following language at the end of the second sentence:

“and (iv) to the Facility Agent for the account of each HK Dollar Lender, the principal amount of each HK Dollar Loan of such HK Dollar Lender as provided in Section 2.09.”

SECTION 3.08 Promissory Notes . Section 2.05(c) (Promissory Notes) of the Amended Facility Agreement is amended by:

(a) replacing the word “or” before “D-3” with a “,”; and

(b) inserting the words “ or D-4 ” after “D-3”.

SECTION 3.09 Fees . Section 2.06 (Fees) of the Amended Facility Agreement is amended by:

(a) deleting the last sentence in sub-paragraph (a) entirely and replacing it with the following:

“Commitment Fees shall be computed on the basis of a year of three hundred and sixty (360) days or (in respect of the HK Dollar Loan Commitments only) on the basis of a year of three hundred and sixty-five (365) days, and shall be payable for the actual number of days elapsed (including the first day but excluding the last day).”; and

(b) deleting sub-paragraphs (b) and (c) entirely and replacing them with the following:

“(b) Facility Set-up Fees . Borrowers agree to pay to the Arranger and the HK Dollar Lender for their own accounts, the administrative fees payable in the amounts and at the times separately agreed in facility set-up fees letters between Borrowers, the Arranger and the HK Dollar Lender (the “Facility Set-up Fees”).

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(c) Agency Fee . Borrowers agree to pay to the Facility Agent and the Collateral Agent for their own accounts, the agency fee payable in the amounts and at the times separately agreed in an agency fee letter between Borrowers, the Facility Agent and the Collateral Agent (the “Agency Fee”).

(d) Payment . All Commitment Fees shall be paid on the dates due, in immediately available funds in US Dollars or any Approved Currency requested by the Facility Agent, to the Facility Agent for distribution, if and as appropriate, among the Lenders. The Facility Set-up Fee with respect to the Singapore Dollar Loans and Yen Loans shall be paid to the Arranger for its own account within five (5) Business Days from August 31, 2007. The Facility Set-up Fee with respect to the Aus