Off-duty Amar Ashraf, 28, was settling down in his seat as a stand-by passenger on the Continental Airlines' flight to Newark when a stewardess suddenly said he had to get off.
Mr Ashraf said he was later told that aviation security chiefs in America had ordered his removal from the jet, even though he has been security vetted for his job with one of Continental's partner airlines.
He believes that the US authorities had decided he was too much of a risk to be allowed on the flight during 10 August heightened alert - because he is a British Muslim as well as being a qualified pilot.
The incident happened as authorities in the US were stepping up the terror alert on flights there from Britain to "severe".
The aircraft had already pulled away from its stand at Manchester Airport and was getting ready to taxi to the runway when he was led down the steps and his bags were removed from the hold.
Mr Captain Ashraf said: "I felt very demoralised when I had to get off.
"As a pilot, you go through lots of security checks and I never would have expected something like this to happen.
"I must have met the profile on the day. I have an Arabic name, I am a Muslim, I'm from the UK and I know how to fly."
Captain Ashraf, from Wrexham, moved to America when he was 18 and has been based there for a decade.
He currently works for one of Continental's partner airlines and was flying back to base in the British Virgin Islands when he was stopped.
He was the only person among a number of stand-by passengers who were asked to leave.
He says he was later told by the Continental Airlines desk that America's Transportation Security Administration, which oversees US aviation security, had asked for him to be ejected.
He was interviewed briefly by the police after the incident.
He said: "I was sitting on the plane as it prepared to take off and had just fallen asleep when the personnel woke me up.
"They asked me to step to one side while they talked to me and said I would have to get off because they weren't taking any stand-by passengers. I didn't believe that."
A spokeswoman for Continental Airlines said it could not comment on individual cases.
America's Department for Homeland Security announced in August it was taking "immediate steps" to increase security on flights to the States from Britain.