A riled-up New York restaurateur got a refund of more than $10,000 from Grubhub after he complained about five years’ worth of bogus fees for phone calls that had nothing to do with food orders, The Post has learned.

The restaurant owner says he first learned about the wrongful charges from last month’s exclusive report in The Post, which detailed how Grubhub has been billing restaurants between $5 and $9 for any call longer than 45 seconds — even if the customer was simply checking on the status of an order, asking what’s on the menu or complaining that the food arrived cold.

At first, the restaurant owner says Grubhub, which also owns Seamless, told him it could only refund him fees going back for 60 days — a line that numerous other restaurants say they’ve also been handed by the company.

“I went ballistic,” said the restaurateur, who asked not to be named for fear of retaliation by Grubhub. “I told them that I wouldn’t accept that.”

After he was handed off to a more senior rep, the Chicago company swiftly agreed to cut him a check for all the erroneous charges going back to 2014, he said.

It’s the largest refund to come to light at a time when other restaurateurs say they are battling tooth-and-nail to persuade Grubhub to cough up more than two or three months’ worth of refunds — or even help them tally what it owed.

“It took them 30 minutes to figure it out,” the restaurateur said of Grubhub. “I guarantee that they know to the penny what their liability is.”

The revelation of the fat refund comes as Grubhub faces a grilling this week from the New York City Council, which has scheduled a Thursday hearing on the fees charged by Grubhub and other delivery services, which restaurants say are cripplingly high.

The restaurant owner shared his story with city council members and other restaurant owners last week, but asked not to be identified while he weighs whether to testify at the hearing. Like other restaurateurs, he’s concerned that Grubhub will retaliate by raising his rates or burying the visibility of his restaurants on the Grubhub site.

“I’ve spoken with a lot of people who fear retribution,” Andrew Rigie, executive director of the New York City Hospitality Alliance, told The Post. “They are concerned about how their fees will be impacted.”

Other restaurateurs are taking their chances, including George Tenedios, who owns 32 eateries in the city, including 18 Fresh&Co outlets.

Tenedios says he will testifying about “bogus phone charges and rate increases” at the hearing, which is spearheaded by Bronx Councilman Mark Gjonaj, who chairs the council’s Committee on Small Business.

Over the past several weeks, Tenedios and a colleague have spent 30 hours each combing through their records to learn how much they’ve been overcharged, he told The Post, “and we’re not done.”

“We look forward to engaging with the City Council and other stakeholders on how we can continue to help restaurants grow their business,” Brendan Lewis, Grubhub’s vice president of public affairs, said in a statement to The Post.

“We’ve not been asked to refrain from taking action against anyone who speaks publicly at the hearing, nor would we engage in any retaliatory acts. We deeply value our relationships with restaurants,” Lewis added.

Even as the City Council plans to grill Grubhub over fees, which some restaurateurs say can be as high as 30% for a food delivery, eatery owners tell The Post the company continues to jack up prices.

One Midtown deli owner who has paid a 12% commission for many years was just informed last Friday that his new rate is 15 percent, according to an email reviewed by The Post.

He intends to fight the fee, he said.