Exhibit
31.2



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

SECURITIES
EXCHANGE ACT OF 1934



I,
Alexander K. Arrow, MD, certify that:



| | 1. | I
    have reviewed this annual report on Form 10-K/A 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;                          
| |    |                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                         
| | 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;                                             
| |    |                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                         
| | 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;
| |     |                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                            
| | (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                                                                                                    
| |     |                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                            
| | (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.                                                                                                                                                                                 



|April 5, 2018 |        | /s/
    Alexander K. Arrow, MD
|------------- | ------ | ------------------------------
|              | Name:  | Alexander
    K. Arrow, MD    
|              | Title: | Chief
    Financial Officer