Exhibit
31.1



CERTIFICATION
PURSUANT TO RULE 13a-14(a) OF THE

SECURITIES
EXCHANGE ACT OF 1934



I,
Garo H. Armen, PhD, certify that:



| | 1. | I
    have reviewed this quarterly report on Form 10-Q of Protagenic Therapeutics, Inc..                                                                                                                                                                                                                                                                                                                                                                          
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| | 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;                                                                                                                                            
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| | 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 registrant as of, and for, the periods
                                                         presented in this report;
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| | 4. | The
    registrant’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 registrant 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 registrant, 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;
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| | (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;                                                                                                                
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| | (c) | Evaluated
    the effectiveness of the registrant’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                                                                                                                                                                                                                                                                                                                                                                   
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| | (d) | Disclosed
    in this report any change in the registrant’s internal control over financial reporting that occurred during the registrant’s
    most recent fiscal quarter (the registrant’s fourth fiscal quarter in the case of an annual report) that has materially
    affected, or is reasonably likely to materially affect, the registrant’s internal control over financial reporting;
    and                                                                                                                                                                                                                                                           



| | 5. | The
    registrant’s other certifying officer and I have disclosed, based on our most recent evaluation of internal control
    over financial reporting, to the registrant’s auditors and the audit committee of the registrant’s board of directors
    (or persons performing the equivalent functions):
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| | (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 registrant’s ability to record, process, summarize and report financial
    information; and
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| | (b) | Any
    fraud, whether or not material, that involves management or other employees who have a significant role in the registrant’s
    internal control over financial reporting.                                                                                                   



|May
    15, 2019 |        | /s/
    Garo H. Armen   
|---------------- | ------ | ------------------------
|                 | Name:  | Garo
    H. Armen, Ph.D.
|                 | Title: | Executive
    Chairman