First-half goals from Sinan Bytyqi and Brandon Barker earned the victory, which could have been more flattering for Patrick Vieira‘s side on another day.
Undoubtedly though, the boy blues will be pleased with their display, as the result rarely looked in doubt once the deadlock had been broken.
Eager to continue their fine form and claw revenge for last season’s defeat to the Cottagers, Vieira made three changes from the side that overcame Liverpool in a thrilling encounter last time out.
In came Jose Angel Pozo for Thierry Ambrose, while Angelino and Pablo Maffeo replaced Matthias Bossaerts and Jordy Hiwula, who made the temporary move to Yeovil earlier in the week.
In the knowledge they could climb to the top of the Barclays Under-21 Premier League with three points, City sought the perfect start.
After just two minutes, Barker embarked on a trademark solo run before firing wide of the target.
It was a statement of intent from the visitors but that effort proved to be the only real chance of the opening 20 minutes, as neither side gained a foothold in the game.
With Fulham employing a physical approach and City attempting to play the passing game, the two teams cancelled each other out somewhat.
As a result, the opening exchanges brought very few chances in an even encounter at Motspur Park.
Moussa Dembele proved to be the hosts’ main threat but fired off-target before a poor touch let the ball roll through to Ian Lawlor when the young Frenchman looked to be through on goal.
City hit their stride just before the half-hour mark. Olivier Ntcham, who scored in the midweek win over Roma in the UEFA Youth League, saw an effort deflect wide off Bytyqi as the away side pressed for an opener.
They were rewarded shortly after as set-piece specialist Bytyqi stepped up to bury a free-kick into the back of the net from 25 yards out, breaking the deadlock.
The home side responded well, seeking an immediate equaliser - and they almost got one but Stephen Arthurworrey headed wide.
It proved to be a costly miss as just minutes later, City doubled their advantage. This time, it was a fine individual effort from Barker, who skipped past a number of challenges before finding the net.
The two quick-fire goals were no more than the visitors deserved, highlighting the attacking prowess of Vieira’s side, who took their two-goal cushion into the break.
City continued where they left off after the restart, as the two goalscorers sought to double their personal tallies.
Bytyqi saw an effort saved before Barker shot wide, while Pozo also tried his luck but sliced well wide.
With the away side in full flow and seeking a third, the Cottagers’ defence were kept busy. Marek Rodak was forced into another fine stop to deny Angelino before Vieira opted to make a change in a bid to net again, as Ambrose replaced Barker.
The striker almost made an instant impact but miscued a header from five yards out. He then attempted an acrobatic effort that flew well off-target.
With the result all but secure, the visitors eased off as the clock ticked down, allowing Fulham to mount some pressure in the dying minutes.
Ange-Freddy Plumain saw two headers blocked - one by the City defence and another by the fingertips of Lawlor.
That was the closest the Cottagers came to finding a consolation though and the away side held on for another fine win to take into the international break.
Next up for Vieira’s men is a European under-19s clash at CSKA Moscow on Tuesday 21 October.
