The young Foxes have now won three, drawn one, and lost just a solitary game in the U18 Premier League South division since the turn of the year, nudging them up to fourth place.
While Catalin Cirjan fired the Gunners into an eighth-minute lead, City's youngsters were ahead just after the hour-mark as first Terell Pennant and then Kasey McAteer turned the game on its head.
Zane Monlouis equalised for Arsenal shortly afterwards, but Leicester once again regained the ascendancy before the interval with Shane Flynn putting them 3-2 up on the 44th minute in Colney.
In the second period, the visitors began to take control with Will Russ adding his name to the scoresheet after 50 minutes, before another from Pennant made sure with two minutes to play.
It's a result which sends City up to fourth in the U18 Premier League South standings, although such is the competition in the top three, third-placed West Ham United hold a 10-point advantage.
Next Saturday, the young Foxes return to Belvoir Drive to tackle bottom side Swansea City (11am kick-off) before travelling to second-place Chelsea on Saturday 14 March (12pm kick-off).
The details...
City: Bosworth; Sams, Barrett, Aisthorpe, Ewing; Flynn, Pennant, Loughlin, Godsmark-Ford; Russ (Fitzhugh 73'), McAteer (Marcal-Madivadua 83')
Subs not used: Odunze, Kutshitnza, Tavares
Goals: Pennant 10', 88', McAteer 31', Flynn 44', 50'
All times GMT.