The u18s boss felt as though his side deserved to win by more goals following an excellent performance at Fratton Park.
Brahim Diaz was the hero for Wilcox’s boys as he scored a late winner to set up a fourth round clash away at Leeds United.
Wilcox told mcfc.co.uk: “I thought we were fantastic, if we’d have won by five or six goals I don’t think anyone would have complained because we were excellent from start to finish.
“Maybe we could have gone in three goals up at half-time as our play was exceptional but it’s a funny competition, like any cup competition, you need to show a bit of character and we had that in abundance.
“Full credit to Portsmouth though, they came into the game second half, scored a goal and gave a good account of themselves.
“We’ve got Leeds in the next round, one of my former clubs, so I’m really looking forward to that.”
Brahim has burst onto the scene in recent weeks, netting a sublime equaliser against Borussia Monchengladbach in the UEFA Youth League last week before netting with another incredible solo effort on the South Coast on Tuesday night.
Wilcox was effusive in his praise for the 16-years old, but urged the Spanish playmaker to continue working hard in order to fulfil his “huge” potential.
“He’s a fantastic young player with huge potential but that’s just what it is at the moment, potential,” Wilcox mused.
“What I will say is he’s a tremendous boy to have around - he works extremely hard every day and he is a special talent but he knows as well as anyone that he’s still learning – he’s a young boy and we’ve got to take care of him.
“The way he conducts himself is an example to any young player but I thought that the lads who dropped down from the EDS were excellent too. They don’t train together all the time – they’ve only trained together for the last three or four days but they’ve given me everything in terms of focus and concentration.”
Lukas Nmecha scored the opening goal in the victory and set up the winner for Brahim.
The England youth international believes that City have every reason to believe that they can go one step further in this year’s FA Youth Cup after they were beaten finalists last time out.
He added: “I’m quite pleased with my performance but it could have been better – it wasn’t my day in front of goal, I thought I could have scored some more goals.
“Leeds will be a good test but we’ve got to back ourselves to have enough to go there and win. We’ve got good enough players to win the competition and we work hard, so why not?”
City u18s are next in action on Saturday when they travel to Stoke City’s Clayton Wood Training Ground.