The comedian served as a judge on this year's run of the ITV competition opposite Amanda Holden, David Hasselhoff and - for the live shows - Simon Cowell.
ITV has now confirmed that McIntyre will not return for a second series. He is believed to have quit in order to focus on a UK stand-up tour.
"We wish him all the best and look forward to working with him again," an ITV spokesman said.
Cowell added: "It's been amazing working with Michael - I don't need to wish him any luck with the tour because it's already gigantic!"
Pregnant Holden was asked on Twitter if she would also be leaving, but replied: "I am going nowhere."
McIntyre is quoted by The Sun as saying: "I absolutely loved being a judge but have been itching to get back on stage myself. I wish the show and production team every success."
A source added: "Michael has been weighing it up for a while as he does like the show and enjoyed being on the panel, but his first love is comedy and he wanted to embark on a tour and concentrate on that."
McIntyre joined Britain's Got Talent at the end of 2010. It is not yet known who will replace the Comedy Roadshow star on the programme.
It was recently alleged that fellow judge Hasselhoff's position on the ITV1 talent show was under threat, although Cowell later insisted that no decisions have been made on the make-up of next year's panel.
Little Britain's David Walliams has been linked with the talent contest in recent weeks.
> Michael McIntyre plans Christmas Comedy Roadshow