Starting in the New Year, Clarke will be responsible for overseeing a range of shows, such as Derek, Black Mirror and Bad Sugar, along with talent initiatives including 4Funnies and Comedy Blaps.
He is currently head of comedy and entertainment at Objective Productions, where he set up the comedy department in spring 2003 after producing the first series of Peep Show.
Clarke has overseen various scripted comedy formats for Objective, including Fresh Meat, Peep Show, Star Stories and Pete Versus Life.
Previously, he was editor of comedy for Talkback Productions, working on various hit shows such as Bo Selecta, Never Mind The Buzzcocks, Big Train and the Brass Eye Special. He started his career at the BBC in both radio and television.
"Phil has been behind some of the biggest comedy hits on British TV," said former BBC One controller Hunt.
"He is brilliantly creative and will be a strong, thoughtful leader for the Channel 4 comedy team."
Clarke said that Channel 4 has an "outstanding comedy heritage", and he is "honoured and delighted to be joining the creative commissioning team".
Nerys Evans, the Channel 4 comedy commissioning editor who has been acting head of the department, will be promoted to deputy head of comedy with "immediate effect".