The Cottagers who were without key forward thinking men Aleksander Mitrovic, who has 27 Championship goals this term and Harry Wilson, knew they were always going to be in for a tough task against a side that were competing for a spot in the play-off places.
This was shown when under a minute into the game, D'Margio Wright-Phillips netted his first senior goal in his first home league start when he converted home from a Josh Tymon cross.
The lead lasted a matter of seconds when Rodrigo Muniz blasted home on the turn before the visitors went ahead just after the half hour mark through a Fabio Carvalho scuffled shot that came off the post and found its way over the line.
Stoke thought they had done enough to settle for a point when a Lewis Baker wonder-strike found its way into the corner for his first goal in a Potters shirt.
However, it wasn't to be as Bobby Reid ensured all three points were going back to the London based side when he smashed the ball into the roof of the net with 18 minutes remaining.
This result sees Fulham earn a fifth consecutive victory, while Stoke drop down to ninth and see themselves suffer a third successive home league defeat for the first time since October 2019.
Story of the game
After making only one change following their win at Hull City, the Potters made a dream start and were ahead in under a minute in what was a memorable moment for Wright-Phillips.
Tymon with time down the left, whipped a delicious ball into the area and on the end of it was the former Manchester City academy graduate who guided the ball first time past Marek Rodak.
The celebrations didn't last long though as moments later the Cottagers were level with Muniz making a case for why he should be being utilised more often.
Harrison Reed played the ball into the 20-year-old and inside the area on the turn, he fired the ball into the roof of the net for his fourth goal of the season, in what was his only second league start for the club.
Four minutes later in what was a lightning start to the match, Stoke were so close to regaining the advantage, but Jacob Brown just couldn't adjust his feet in time to tap home Wright Phillips' low drive across the box.
After the hectic opening ten minutes the game started to settle down with Fulham maintaining control without causing too many problems for Michael O'Neill's back three.
However, 12 minutes before the break Fulham's dominance in possession did pay off when Carvalho, who is linked with a move to Liverpool, netted home to turn around a one goal deficit.
Reid got down the right hand side and he cut the back to a free Carvalho whose scuffed shot dribbled off the post and over the line, despite the efforts of Taylor Harwood-Bellis to seal a fourth goal in three games for the 19-year-old.
Seven minutes later, Muniz will have felt that he could have doubled his personal tally for the day when he was found from a Reed free kick from the left, but his header had no direction on it as it was easily held by Jack Bonham.
At the start of the second period, Marco Silva's side continued in the same fashion that they ended the first half in and were close to extending their lead two minutes after the interval.
After neat intricate play on the edge of the box, Carvalho slipped in Kenny Tete down the right, but from close range Bonham did well to block out the full back's effort.
Although, with Stoke growing back in the game they did level affairs inside 58 minutes when Baker from distance smacked an effort goalwards that evaded Rodak and nestled into the right hand corner, erupting the home fans into life.
Despite the Potters leveller seeming to boost them with confidence, they were set another setback when Reid, against the run of play, regained the Cottagers’ lead.
From a corner from the right, Muniz saw his powerful header cannon off the crossbar, but when Baker failed to clear, Reid capitalised by smashing the ball first-time into the roof of the net for his third goal of the campaign.
The home side kept on fighting though and were inches away from nicking a point when from off the bench on his debut after joining on loan from Aston Villa, Jaden Philogene-Bidace deflected low effort from the left beat Rodak, but rebounded off the post.
Two minutes later, the 19-year-old came close again with him this time bursting down the left, but his powerful strike was fired narrowly over the bar as it just didn't turn out to be Stoke’s day.
Encouraging signs for Potters despite defeat
Despite coming away from the clash with Fulham with no points, O'Neill can come away with pride especially with the second half showing and will feel slightly hard done that they have not come away with something.
What will particularly please the former Northern Ireland boss is the performances of the new additions to the squad, as two players that were starting in their first home league game for the club netted, in Wright-Phillips and Baker.
Baker especially impressed throughout with him playing in the heart of midfield with the former Chelsea player getting involved and looking to win every individual midfield battle when being forced to defend.
Then when on the attack he was looking to provide support and an extra body in the box and it can't be forgot his sweet strike that nearly earned the Potters a point.
Another new signing that staked a claim was Philogene-Bidace who even though came off the bench, was difficult to get the ball off down the left hand side and he looked a threat in the latter stages of the game.
The only things that the Aston Villa youngster could have improved upon is the finishing touch, but that will come with time experience at the senior level.
Star Player- Rodrigo Muniz
Since joining in the summer from Flamengo, Muniz has struggled to break into the starting lineup ahead of the prolific Mitrovic, as prior to today, the Brazilian had only made one league start which came back in November.
Then when provided the opportunity by Silva, he certainly took it as he caused problems for the Potters backline all afternoon in the solo striker role especially with his ability in the air and his consistency to find himself inside the area.
Then when a chance came his way, the 20-year old didn't need asking twice as when given half a yard he convincingly smashed the ball past Bonham to level the game early on.
Overall, Muniz's showing will certainly please Silva and give him confidence in his depth in the forward areas as Fulham look to see the comfortable position they currently find themselves in the Championship.