Freddie Sears scored in the opening 16 seconds as Ipswich made it seven games without a win for Fulham.
The visitors took an early lead in the Championship game when Sears ran at Fulham’s defence from the kick-off and fired home from the edge of the box.
The Cottagers were level when Ross McCormack struck a fantastic 30-yard free-kick into the bottom-left corner.
But Ipswich scored the winner in the second half when Brett Pitman steered home Sears’ cross.
Town remain sixth in the table, with Fulham – the top scorers in the division with 34 goals despite being held scoreless on Tuesday night – staying 17th.
It was the second game in charge for Cottagers senior coach Stuart Gray, after their 2-2 draw with Brentford, as the club continue to look for a new manager following Kit Symons’ departure in November.
Fulham had chances to level with substitute Matt Smith heading just wide, but at the other end Sears put a shot just wide for Ipswich.
After that chance, the hosts never looked like forcing a late equaliser.