Clarke missed most of the current campaign due to an ankle injury suffered during Northampton's opening Guinness Premiership game against Newcastle last September.
Clarke's new deal supercedes his existing contract, which had one more season to run, and he will remain at Franklin's Gardens until 2010.
He said: "Obviously, it was a hard season for me after the injury and not being able to help the lads on the field, but the club stood by me and the medical team were brilliant throughout my rehabilitation.
"I am looking forward to helping get Saints back to the Premiership at the first attempt, and then to the top of English rugby."
Northampton were relegated into National League One almost two weeks ago after finishing one point beind Worcester in the Premiership survival fight.