Dara O'Briain will return as host of the satirical news quiz, with its panel members drawn from the world of comedy.
Angst Productions series producer Dan Patterson said: "Frankie has been a brilliant member of the team since the beginning and the door is always open for him to come back. We wish him all the best with his other projects."
In his newsletter, Boyle said: "And finally, I've decided not to do any more Mock The Week. I've done what feels like a good few thousand of them now and I feel I've mocked the s**t out of the week.
"I salute everybody there (salutes). I'm going to concentrate on next year's tour and some other funny things I'm writing. Be careful out there everybody. Heil Hitler."
BBC Two controller Janice Hadlow said: "Mock The Week is a major part of the BBC Two schedule, regularly delivering wit and energy to an enthusiastic audience.
"This two series commitment shows just how much we value it."