Meals at a Shake Shack on the Upper East Side are responsible for more upset stomachs than any other restaurant in the city, 311 complaint records show.

The busy East 86th Street and Lexington Avenue location has racked up 11 complaints over the last year out of a total of 3,220 — more than any other Big Apple eatery.

On March 24, a diner experienced “abdominal cramps” from a burger bought at the restaurant, city records show.

The company has “long suspected that a former employee was behind a series of phony complaints following termination from the company,” said spokesperson Edwin Bragg.

The New York City-founded burger joint also piled on an additional five complaints from locations across Manhattan and Brooklyn. Bragg declined to comment on the complaints at the other restaurants.

New York’s second-most-nauseating fare can be found at a restaurant behind security at Kennedy Airport’s Terminal 8, the complaint records show.

Brooklyn comedian Matt Ott, 30, recounted his stomach-churning experience on Christmas Day at the terminal’s Brooklyn Deli.

“It was the first thing I ate really early in the morning when I got a fever, chills and diarrhea,” he said. “It was the worst. Nothing like having food poisoning from airport food on Christmas.”

A spokesperson for Brooklyn Deli declined to comment.

Third on the complaint list is the hot buffet at Whole Foods in Gowanus. Whole Foods also declined to comment.

Health Department inspectors check the 311 complaints and launch investigations, but many of these probes are closed without action due to a lack of evidence.

“If the complainant is anonymous, there’s no way for us to follow up,” said Health Department spokesman Jeremy House. “So there has to be enough information in the complaint, as well as a

cluster of reports in order to initiate a field investigation.”

Food testing also can lead to a dead end.

“In most cases we can’t determine if the food was actually contaminated because the food from that day was thrown away,” House added.

The Health Department could not provide an exact number of confirmed foodborne outbreaks and was unable to comment on the volume of Shake Shack complaints.