One of the students suffered a cut lip, and the other sustained a bruised and swollen head during the Jan. 28 incident at P.S. 65 in the Ozone Park neighborhood, prosecutors said.
After the boys began fighting, prosecutors said, Gullotta told a third student to close the classroom door. Gullotta then instructed the other students to back up to give the boys room to fight, prosecutors said.
When Gullotta sent one of the boys to the school nurse two periods later, authorities said, he told him to lie and say he was hurt by bumping into another student while trying to pick up a pencil from the floor. The nurse later summoned the other boy, prosecutors said.
Authorities said they learned about what happened after one of the boys' parents overheard him talking about it.
Gullotta and Abraham Fox, a teacher's aide who prosecutors say witnessed the incident, are charged with two counts of endangering the welfare of a child, a misdemeanor. If convicted, each faces a maximum one year in jail.
The men were arraigned in Queens Criminal Court on Saturday. A judge released them on their own recognizance. They're scheduled to return to court Feb. 25.
Gullotta, 29, of Long Island, has been reassigned outside of the classroom, said Department of Education spokeswoman Margie Feinberg. Fox, 43, also of Long Island, has been suspended without pay, she said.