Rotherham United suffered another defeat, leaving them at the foot of the Championship table.
Former Miller Ben Pringle put the visitors in front and Ross McCormack made it two from the penalty spot on 16 minutes.
Matt Derbyshire saw a penalty saved after 55 minutes before Jonson Clarke-Harris fired a goal back on 72 minutes.
Fulham sub Cauley Woodrow finished the game off four minutes into injury time.
“We made two or three errors for each of the Fulham goals,” said Millers boss Steve Evans.
“We created two or three good chances in the first half and didn’t take them. We huffed and puffed in the second half.
“It’s evident after the games we’ve played that there’s a lot of work that needs to be done."