Kongolo, 26, joined the London side on loan in January but suffered a broken foot and returned to the Terriers after making just a single appearance.
The Dutchman joined Huddersfield from Monaco for a club record £18m fee in 2018 and played 60 games for the club.
Kongolo said: "I am really happy. It has been a while, been waiting the whole day, but the end result is I can play for Fulham. I am proud to be here, and I will give everything for this club."