Owen Coyle admitted the better side won last night at Craven Cottage, but Bolton's cause was not helped by injuries to key players.
Fulham ran out 3-0 winners in west London thanks to a double from Clint Dempsey and a header from Brede Hangeland, with three points easing their faint relegation fears.
Bolton could have climbed to seventh with victory yesterday, but had to travel back to the north west counting the cost of a hectic schedule.
And, although Coyle was not out to make excuses, the Bolton boss was keen to point out that injuries had played their part in the result against Mark Hughes' side.
"We came here looking to build on the great result and performance against Arsenal on Sunday and we started the game really well. We had the first real chance of the game but we didn't take it," he said.
"We know Fulham are a good side at home and we conceded three goals from set-plays, which was disappointing.
"It's not helpful with [Daniel] Sturridge missing, [Gretar] Steinsson twisting his knee and [Stuart] Holden’s still a big loss.
"It was a fantastic result at weekend, the thing about Sunday was we gave a big performance on the back of the disappointment from the week before. Tonight was going to be a big ask, both physically and mentally, when the goal went in it changed the game, goals change games.
"They're soft goals we’ve conceded, taking nothing away from Fulham."