A blustery wind coupled with a hard bouncy pitch caused both sides problems as the Gills and Orient shared the points at the Ford Sports Ground on Saturday.
From the kick-off Gillingham kept the ball well in the first half and in the view of Manager Mark Patterson, "performed as well as we have played for a long time."
The visitors created the better of the early openings and could have taken the lead in the 15th minute as Liam Geering's cross carried to Dean Rance in the box but the midfielder headed straight into the keeper's arms with the goal at his mercy.
Gillingham were on top of the game and went close with a couple of half chances whilst at the other end restricting the O's to one solitary shot which saw their winger cut in to the box before firing harmlessly into the side-netting.
The Gills duly took the lead in the 25th minute with a well worked move that originated from keeper Conor Quinn and saw a patient build-up before Charlie Stimson flicked Tom Brunt's neat pass through for Tom Murphy to tuck his finish under the advancing keeper.
The visitors continued to control the game until the interval but a change of ends brought a contrast in fortunes. Orient changed their shape to disrupt Gillingham's passing style and the game became a far more evenly balanced affair.
That said, neither team seriously troubled either keeper and the game seemed destined to fizzle out at 1-0. Then, from their only serious chance of the game, Orient fashioned an equaliser. The Gills had their chances to clear in the build-up but were punished for their complacency when Jake Argent slotted home despite the best efforts of keeper Quinn.
Two minutes into injury time a good cross from the right by Ollie Bartrum was nodded on by Rance to Callum Day but he snatched at his shot and put it over the bar, spurning the chance to seal the win.
The result, together with last week's 3-0 beating of Peterborough, keeps Gillingham top of Youth Alliance Cup Group 4 and Manager Mark Patterson is encouraged to see his team performing well in a tournament they reached the semi-finals of last season, "The passing and movement and the general football in the first half was excellent. So I was very pleased with that"
"The lads were really disappointed afterwards because they know that they played well enough to win the game. But it keeps us on top of the group and there were some excellent individual performances. Tom Brunt was outstanding in centre midfield, the two centre-halves played really well and Quinny, the goalie, had an excellent game."
Gillingham: Conor Quinn, Ollie Bartrum, Connor Essam, Callum Davies, Jack Evans, Liam Geering, Tom Brunt, Dean Rance, Alex Brown, Charlie Stimson (80 Callum Day), Tom Murphy
Subs not used: Daran Hawkes, Josh Sargeant, Aaron Beckles, Ryan Benniman.