Two goals either side of the interval helped put paid to the Academy team's hopes of taking anything from their trip to Fulham at the weekend.
The Molineux youngsters hit back through Andre Landell, this after missing a penalty, before a Fulham break saw a third goal confirming the win for The Cottagers.
Coach Mick Halsall said: "It was a good competitive game and I thought the players came out of it with a lot of credit. It was always going to be tough and from the start we were asked questions.
"It took us a while to settle down into some sort of rhythm of play but after 15 minutes I thought we were in the game.
"Although they had more possession than us, we worked well at closing their space and trying to keep them in front of us.
"I think we had the two best chances in the first half and with more accurate shooting from Liam McAlinden and John Gorman we could have taken the lead.
"But it wasn't to be and we conceded from a set play just before the break with their player getting on the end of a deep cross to the back post
"The half time team talk was all about making sure the players realised we were still in the game but within two minutes of the second half we were 2-0 down.
"We responded well and forced a clear cut penalty but, unfortunately, McAlinden missed from the spot. But we continued to press forward and eventually scored through Andre Landell.
"We showed good commitment to get forward creating at least another six decent chances but we could not finish. Then Fulham broke to the score 3-1.
"Again we continued to get at them but could not succeed in breaking them down.
"I feel we learned more from this game than from the victory against Ipswich last week. This was hard all the way through but the players stuck at it and, in the end, I thought they did well."