Exhibit 31.1

CERTIFICATION OF CHIEF EXECUTIVE OFFICER

I, Arthur H. Penn, Chief Executive Officer of
PennantPark Investment Corporation, certify that:

1. I have reviewed this Report on Form 10-Q of PennantPark Investment Corporation;

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 consolidated 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)) and internal control over financial reporting (as defined in Exchange Act Rules 13a-15(f) and 15d-15(f)) 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 subsidiaries, is made known to us by others within those entities, particularly during the period in which this Report is being prepared; and

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 consolidated financial statements for external purposes in accordance with generally accepted accounting principles; and

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 the end of the period covered by this Report 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 period covered by the annual report 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, 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.

Dated: August 7, 2013



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|/s/ Arthur H. Penn     
|Arthur H. Penn         
|Chief Executive Officer