The "Mystic Pizza" restaurant in Mystic was not where the movie was filmed. Only one scene of the movie was actually filmed in Mystic village, which was the scene where the fishing boat was going through the draw bridge. Mystic is a popular tourist destination that would have been too crowded for filming a movie so the filming was done in the sleepy neighboring town of Stonington, CT. They used a business on Water street for restaurant filming, and in the early part of the movie there is a scene where a pizza is being delivered via motor scooter, where they go past the town green where the two old cannons are on display.
Mystic Pizza is a real pizza parlor, located at 55 West Main St. in Mystic, Connecticut. Writer Amy Jones was vacationing in Mystic one summer, saw the pizza parlor and was inspired to write the story. After the movie came out, the real Mystic Pizza shop became so popular, lines would stretch to the sidewalk and patrons would regularly steal mementos from the restaurant.