Former owner Mohamed Al Fayed, a close friend of the late performer, commissioned the statue which was erected outside the west London stadium in April 2011.
The memorial for a man that only visited the ground once shocked many, but Khan promised to get fans' views rather than make a "knee-jerk reaction" after completing his takeover of the club.
Al Fayed warned Khan he would be "in big trouble" if it went, promising to shave off his moustache, but the new owner has decided to take the statue down.
"Craven Cottage means the world to generations of Fulham supporters, and I have heard from many of them over the past two months," he said in a statement on the club's official website, www.fulhamfc.com.
"Our supporters' views on the statue have been made clear.
"I respect Mr Al Fayed and know he had good intentions in paying an individual tribute. However, the removal of the statue is the right thing for Fulham Football Club."
The statue was commissioned following Jackson's death in June 2009 and was due to be erected at Harrods before Al Fayed sold the Knightsbridge store.
The decision to relocate it to Craven Cottage was controversial, with statues at football grounds generally reserved for club legends.
Jackson's links to Fulham are tenuous to say the least - he watched a game against Wigan there as a guest of Al Fayed in 1999 - while the singer was also dogged by controversy during his lifetime.
Source: PA
Source: PA