Meulensteen worked at Manchester United alongside Sir Alex Ferguson from 2007 to this summer when he left the club.
The Dutchman had been linked with the vacant Crystal Palace job.
Fulham chief executive Alistair Mackintosh said: "We’re all delighted to welcome Rene to Fulham.
"There was always going to be a battle for Rene’s services and, with the assistance of our Chairman Shahid Khan, we’ve been able to bring one of the best coaches in the world to Fulham."
Meulensteen added: "I was impressed by the vision of Shahid Khan and Alistair Mackintosh.
"I’ve spent many hours talking with Martin Jol and we share a vision of how football should be played and how players should be developed. It’s our job to make sure we can bring this vision to life on the pitch for the fans."