City left Vicarage Road with a 2-0 win and a place in the fourth round of the competition which will see us travel to West Ham in January.
A fortunate first-half goal from Matty Warhurst was solidified by a Jaden Heskey strike early in the second half to top off a lively performance.
And Wilkinson praised the performance of Mfuni who was also tasked with playing out of his favoured position of centre-back.
“He’s an exceptional talent,” exclaimed Wilkinson when asked for his thoughts on his youngest defender.
“We think very highly of him. For a player that’s 15 years old, he has great maturity and a real high level of potential.
“He played slightly out of position tonight at left-back but dealt with the ball really well and looked comfortable in defensive situations.
“There are still some things we saw and think he could have done better but for a 15-year-old to sort of step into this environment and look so comfortable is a really positive sign.”
In the latter stages of the match, the hosts looked to keeps their ambition of progressing to the next stage of the competition alive with overloading attacks.
But City’s defensive line of Ezra Carrington, Jahmai Simpson-Pusey, Lakyle Samuel and Mfuni were a formidable force considering it was their first time playing together as a four.
And Wilkinson was full of praise for not only his defenders but his whole team who performed well against a tough Watford team.
“It was a difficult game, Watford are a good side, they’ve played some really good teams recently and looked like a very competent outfit,” said Wilkinson.
“To win away from home and with a really professional performance, I thought the lads played well, we had really good control of the game for long parts and looked a constant threat.
“I also thought we were solid at the back so it was quite a pleasing performance by the team.”
City’s next FA Youth Cup appearance will see us travel to West Ham on Friday 12 January. More details about the fixture will be provided on mancity.com.