The case was filed in the court of Chief Judicial Magistrate in Muzaffarpur district.
The court has fixed July 16 for the hearing.
Prakash Kumar, a resident of Pokhraira village, said Modi insulted the national flag on International Yoga Day (June 21) by using it as a mere piece of cloth, sat on it and also used it to wipe his hands and face.
"Modi's acts were an insult to the national flag and it hurt millions in the country," the petitioner said.
He has also submitted a series of pictures downloaded from the internet as evidence in support of his petition.