The Dutchman had led the Cottagers on a disappointing run of results and the London side are currently in the relegation zone in the Premier League.
"I am disappointed in this season but know there are better days ahead for Fulham and its supporters," Jol told the club's official website.
"It was a privilege to manage Fulham, one of the great clubs in the Premier League or anywhere in the world.
"I will always treasure my experience here and want to thank Mr. Khan and everyone at Fulham for the opportunity."
Fulham host Tottenham Hotspur on Wednesday.