The midfielder opened the scoring and made City's second to heap more misery on Fulham boss Chris Coleman, whose side are dragged deeper into relegation trouble.
Four months ago, Coleman was being lauded by the Fulham faithful for masterminding their victory over Arsenal.
But talk of reaching a place in the UEFA Cup proved premature and now the fans at Craven Cottage are calling for his head.
It looked like it could have been Fulham's day for they started brightly enough. Simon Davies first tried his luck from distance but saw his shot in the eighth minute drift narrowly wide.
Alexei Smertin was then denied by an excellent finger-tip save by Andreas Isaksson in the 17th minute.
But just as Fulham were beginning to settle, Barton caught them napping and struck with deadly effect.
Emile Mpenza out-muscled Moritz Volz before racing at the heart of the Fulham defence. The striker picked out Barton, who cut inside before drilling a low shot past Antti Niemi in the 21st minute.
Matters soon became worse for Coleman, as City strolled into a 2-0 lead with only 36 minutes gone.
Barton was again involved as he threaded a pass through to DaMarcus Beasley who cut in from the left wing before calmly dispatching a low shot into the net.
Fulham were stunned and a Brian McBride header that went wide did little to signal any kind of a comeback.
City were rampant and Nedum Onuoha was just inches away from giving them a three-goal cushion at the break when he headed wide from a corner.
After a chorus of boos rang out from Craven Cottage to single the half-time interval, Fulham were again quickest out of the blocks at the re-start.
Some neat work between McBride and Heidar Helguson gave the home crowd some optimism, although the two did not manage to force a save from Isaksson.
Then, just as the first half had swung in City's direction, the second followed suit and Stuart Pearce's side were soon 3-0 up and looking comfortable.
A long ball over the top seemed to be easy for Liam Rosenior, but the defender slipped at the crucial time allowing Darius Vassell the opportunity to sneak in and plant a low shot past Niemi.
Coleman turned towards desperate tactics to find Fulham a way back into the game and brought on Tomasz Radzinski, Vincenzo Montella and Clint Dempsey.
His attacking options did put a little pressure on the City back four, but it was Fulham's centre-half Carlos Bocanegra who scored a consolation goal.
The American international climbed highest at the near post to head in from Davies' corner kick.
It was a case of being too little too late for Fulham who sit precariously above the Premiership drop zone. Meanwhile, the win for City eases their relegation fears and takes the heat off Pearce.