A JetBlue pilot forced a Manhattan man to sit on the toilet for three hours during a cross-country flight to free up his seat for a stewardess, the flush-with-fury passenger charges in a $2 million lawsuit filed yesterday.

Gokhan Mutlu claims the experience made him feel like a first-class loo-ser – and his Manhattan Supreme Court suit says that he suffered “emotional and psychological trauma” and that the JetBlue crew “publicly . . . humiliated and dishonored” him.

“In the middle of the flight, the pilot told me to go to the bathroom and have a seat,” Mutlu told The Post from his home in upper Manhattan last night.

“I guess the flight was overbooked, and I didn’t want to make a big deal in front of the other passengers, so I just had a seat. “I don’t feel good. I was humiliated.”

Mutlu says the can-finement happened Feb. 23, when he was a standby passenger for a flight from San Diego to New York.

He was told the flight was full, but a stewardess told him that he could take her assigned seat and that she would sit in the “jump seat,” said his lawyer, Zafer Akin.

Mutlu was issued a boarding pass and took Seat 2E, but got a rude awakening as he dozed off about 90 minutes into the red-eye flight, he claims.

The pilot called him to the front and “advised the plaintiff that he would have to give his seat up” to the flight attendant, the suit says.

The pilot told him the “flight attendant wanted to be more comfortable and that the ‘jump seat’ was not comfortable for her.”

A stunned Mutlu asked whether that meant he was supposed to sit in the jump seat for the rest of the five-hour flight, but the pilot told him that would be against regulations, Akin said.

The pilot told him to “hang out” in the bathroom,” the suit says, adding the stewardess took Mutlu’s seat, “closed her eyes and pretended to sleep.

When Mutlu argued, the pilot advised him that “this was his plane, under his command, and that [he] should be grateful for being onboard,” the suit says.

“The plaintiff walked to the back of the plane, trying to hide and cover his face,” and “stepped into the bathroom, closed the door and locked it,” the suit says.

Soon after, the plane ran into turbulence. While other passengers were ordered to buckle up, Mutlu was “sitting on a toilet stool with no seat belts,” the suit claims.

“He was looking for things to hold on to,” Akin said.

After landing, the suit says, the pilot asked Mutlu “if everything was OK.”

“The pilot said, ‘I don’t think you appreciate what I did for you.’ My client said, ‘You locked me in the bathroom,’ ” Akin said.

“I brought you home,” the pilot countered.

Akin said his client would have been happy to wait for a later flight, and probably wouldn’t have sued had the crew let him sit in the jump seat.

JetBlue said it doesn’t comment on pending litigation.

Additional reporting by Christina Carrega

dareh.gregorian@nypost.com