All the goals came in the first half as Fulham stormed to a fourth straight league win, sending a promotion warning to their rivals.
Town went ahead through Chris Lowe's fourth-minute penalty but Scott Malone equalised before Tom Cairney put the visitors ahead from the spot.
Two goals from Stefan Johansen made it 4-1 at the break and there was no way back for Town.
"It may sound ridiculous but I think the start we made probably cost us,” said Town's boss David Wagner.
"Once we scored we were maybe a little bit over motivated and euphoric and showed a lack of concentration.
"We lost focus and concentration and against a team like Fulham, who are such a strong offensive side, we got punished.
"Fulham are a great side and deserved their win but we played a big part with the errors we made.
"It is difficult to win football matches when you concede goals because of individual mistakes and a lack of concentration.
“It is unusual as normally this group is so reliable and I can never moan about the attitude and effort which they show.
"Defeat hurts, of course, but I have been able to trust the players who made mistakes over the whole season and we move on.
"To move on you have to know why you lost and we know why we lost."
Despite the heavy defeat and an overall dip in form, Huddersfield Town still find themselves firmly entrenched in the top six ahead of their visit to Wolverhampton Wanderers on Tuesday evening (7.45pm).
Another win will seal a Play-Off place for Town with Leeds United currently in seventh-place, five points behind with just two games to play.
"It's still in our own hands and we have three games left,” added Wagner.
"We have shown unbelievable consistency all season and we have been in the top six virtually the whole season.
"In my opinion we have been the most consistent team in this division so far."