City's youngsters had lost six in a row in all competitions since the opening-day victory over Derby County in August, so they travelled south to Motspur Park determined to end that run.
Within five minutes in the capital, they were ahead as Wanya Marçal was teed up stylishly by Amani Richards, before Silko Thomas added another four minutes later by calmly beating Alex Borto in the home net.
It was the perfect start for the side coached by Ben Petty, but the home outfit halved the deficit before the break, through Jonathan Esenga's impressive free-kick in the 24th minute.
Chris Donnell hit the woodwork for the Cottagers in the second half, while Richards also hit the bar for Leicester in an entertaining PL2 clash. It was a game which could have gone either way, but the young Foxes were on top.
They made it 3-1 later on, with Kian Pennant finding the net in the 89th minute, after capitalising on a stray back-pass. Richards' penalty was saved by Borto in added time too, but the work was done for Leicester.
City's youngsters are up to 16th in the 26-team Premier League 2 standings and next face Fulham again, this time in the Premier League Cup, away on Friday (7pm BST kick-off).
The details
City: Young, Nelson, Appiah, Wilson-Brown (Godsmark-Ford 75'), Cover, Raikhy, Cartwright (Ali 75'), Hill (Amartey 60'), Richards, Marçal (Pennant 79'), Thomas.
Goals: Marçal 5', Thomas 9', Pennant 89'.
Sub not used: Doherty.