Exhibit 31.1

CERTIFICATION

I, Robert M. Thornton, Jr., the Chief Executive Officer
of SunLink Health Systems, Inc. (the Company), certify that:

(1) I have reviewed this quarterly report on Form
10-Q/A of the Company for the period ended March 31, 2011 (the Report);

(2) Based on my knowledge, this
Report does not contain any untrue statement of a material fact or omit to state a material fact necessary to make the statements made, in light of the circumstances under which such statements were made, not misleading with respect to the period
covered by this Report;

(3) Based on my knowledge, the financial statements and other financial information included in this
Report fairly present in all material respects the financial condition, results of operations and cash flows of the Company as of, and for, the periods presented in this Report;

(4) The Companys other certifying officer and I are responsible for establishing and maintaining disclosure controls and procedures
(as defined in Exchange Act Rules 13a-15(e) and 15d-15(e)) for the Company and have:

(a) Designed such disclosure controls
and procedures or caused such disclosure controls and procedures to be designed under our supervision to ensure that material information relating to the Company, including its consolidated subsidiaries, is made known to us by others within those
entities, particularly during the period in which this Report is being prepared;

(b) Designed such internal control over
financial reporting, or caused such internal control over financial reporting to be designed under our supervision, to provide reasonable assurance regarding the reliability of financial reporting and the preparation of financial statements for
external purposes in accordance with generally accepted accounting principles;

(c) Evaluated the effectiveness of the
Companys disclosure controls and procedures and presented in this Report our conclusions about the effectiveness of the disclosure controls and procedures, as of March 31, 2011 (the Evaluation Date), based on such evaluation;
and

(d) Disclosed in this Report any change in the Companys internal control over financial reporting that occurred
during the Companys most recent fiscal quarter ended on the Evaluation Date that has materially affected, or is reasonably likely to materially affect, the Companys internal control over financial reporting; and

(5) The Companys other certifying officer and I have disclosed, based on our most recent evaluation of internal control over
financial reporting (as defined in Exchange Act Rules 13a-15(f) and 15d-15(f)), to the Companys auditors and the audit committee of the Companys board of directors (or persons performing the equivalent functions):

(a) All significant deficiencies and material weaknesses in the design or operation of internal control over financial reporting which
are reasonably likely to adversely affect the Companys ability to record, process, summarize and report financial information; and

(b) Any fraud, whether or not material, that involves management or other employees who have a significant role in the Companys internal control over financial reporting.



|             |  |                                                     
|------------ |  | ----------------------------------------------------
|May 21, 2012 |  | /s/ Robert M. Thornton, Jr.                         
|             |  | Robert M. Thornton, Jr.                             
|             |  | SunLink Health Systems, Inc.
Chief Executive Officer