Acting Chief Justice V M Sahai rejected the plea of AAP member Nishant Verma.
The HC also set aside the lower court's finding that the offence had been committed but no action could be taken as the petition was filed after a delay of more than one year.
Earlier, Verma's application had been rejected by a magistrate and the sessions court on the ground of delay.
"The petitioner has to explain the reason for delay."
Verma had sought an FIR against Modi for "hiding" his marital status in the affidavit he had filed with his nomination for 2012 Assembly polls (when Modi was the Chief Minister of Gujarat) for Maninagar seat here.
Verma contended that when Modi contested the Lok Sabha election in 2014, he mentioned his wife's name in the affidavit for the first time, disclosing the earlier omission.
Section 125 A(3) deals with concealment of information while filing affidavit and provides for imprisonment upto six months.
