Charlotte Moore - Controller of BBC One - made the announcement this morning (December 2) at a BAFTA session.
Starring Adil Ray as lead character Mr Khan, Citizen Khan first aired in August 2012, with a second series transmitting on BBC One in October and November of this year.
A Christmas special has also been scheduled for later this month, with the third series now expected to follow in 2014.
Moore also addressed the "controversy" surrounding Citizen Khan - with the show having been criticised in some quarters for its depiction of South Asian culture.
"We're not scared of being edgy and provocative in comedy," she said. "Comedy is meant to take us into those areas."
BBC One has also commissioned new sitcom Grey Mates starring Russ Abbot and June Whitfield.
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Watch a clip from Citizen Khan below: