Jay Simpson put Orient ahead with a well-placed header 16 minutes from time, before Blair Turgott extended their lead moments when he provided the finishing touch to a wonderful counter-attack.
Ollie Palmer then grabbed his first goal for the Club in added time to seal a 3-0 victory at the Matchroom Stadium.
Fresh from their win at Dagenham & Redbridge on the weekend, O’s Head Coach Ian Hendon named the exact same 18-man squad for the visit of Teddy Sheringham’s Stevenage.
Orient had taken the lead in all three of their fixtures this season, but with two minutes on the clock it was Stevenage who nearly opened the scoring.
Striker Brett Williams beat the O’s offside trap and unleashed a volley from just inside the penalty area which beat the dive of Alex Cisak, only to come back off the post before hitting the Australian stopper’s back and going out for a corner.
After the early scare Orient settled into the tie however and ten minutes later had their first real opportunity when Frazer Shaw’s deep cross was knocked back by Dean Cox into the path of Paul McCallum.
McCallum, who registered his second goal of the season on the weekend, then turned swiftly on the six-yard line but was denied by a last-ditch challenge from Mark Hughes before heading the resulting corner wide.
With the O’s enjoying the majority of possession it was Cox who had the next opportunity moments after when Bradley Pritchard picked out his run to his right but the midfielder sliced a first-time shot wide.
As the match approached the 30-minute mark controversy struck as Orient looked to have made the breakthrough.
Sean Clohessy was constantly providing an option down the right and the full-back delivered an excellent cross into the box which McCallum met with a header that beat Boro ‘keeper Chris Day but was cleared off the line by Mark Hughes.
McCallum reeled away to celebrate convinced his header had gone over the line but referee Chistopher Sarginson waved play on, although replays showed that the ball had indeed crossed the line.
The O’s appeared to be in control of proceedings but were then saved by woodwork for a second time nine minutes before half-time.
Dipo Akinyemi showed good footwork on the edge of the O’s penalty area to work some space and unleashed a rasping drive that flew beyond the dive of Cisak but crashed off the underside of the bar before being cleared.
Immediately after Orient then had a penalty appeal fall on deaf ears as Jay Simpson saw a shot blocked by Hughes from close range in what was to be the final action of the first half.
Following the interval it was the O’s who had the first chance of the half as Sammy Moore fired a volley over the bar from a Shaw cross.
Five minutes later Cisak was called into to action to make his first save of the night as he dived to his left to parry away Williams’ long-range strike.
Ian Hendon then made his first substitution on the hour as he reverted to a flat 4-4-2 by withdrawing Lloyd James and replacing him with Blair Turgott who took up a position on the right of midfield.
It didn’t take long for the O’s substitute to get involved in the tie as moments after his introduction he delivered a teasing ball into the box that McCallum could only direct over the bar.
Stevenage responded with a substitution of their own as Tom Conlon entered the field and he too found himself at the thick of the action straight away as he drilled a low shot just wide of the far post.
Both sides continued to slug it out and search for that elusive first goal and on the 73rd minute it was the O’s turn to be denied by the woodwork.
Jay Simpson showed brilliant composure inside the penalty area to bring down a Clohessy cross but his powerful shot cannoned back off the post.
A minute later Simpson was not to be denied however as Cox brilliantly worked his way down the left and delivered a brilliant cross for the O’s striker to head into the far corner.
Much like the opening day against Barnet, the O’s then quickly added a second in what can only be described as a spectacular team move.
All starting from a Stevenage corner, the O’s broke quickly in numbers and Moore picked out Clohessy just to the right of the penalty area with an incisive cross-field pass.
The O’s full-back then expertly volleyed the ball back into the middle for Turgott who wonderfully thumped a side-foot volley beyond the helpless Day in the Boro goal.
The scoring was not to end there though as in added time Ollie Palmer grabbed his first goal for the Club.
Having came on for McCallum for the final 15 minutes, the forward capitalised on a Boro mistake as he ran onto Dean Wells’ loose back-pass and beat the best efforts of Day to poke home a third and move Orient up into top spot.
ORIENT: Cisak, Clohessy, Essam, Baudry (C), Shaw, James (Turgott 60), Pritchard, Moore, Cox (Dunne 82), Simpson, McCallum (Palmer 75)
SUBS: Grainger, Ling, Moncur, Kashket
GOALS: Simpson (74), Turgott (85), Palmer (90+1)
BOOKINGS: Simpson (60)
STEVENAGE: Day, Franks, Wells, Hughes, Okimo, Pett (Storer 79), Lee (Conlon 64), Schumacher (C), Parrett, Akinyemi, Williams (Hitchcock 75)
SUBS: Kettings, Casey, Ogilvie, Gorman
BOOKINGS: Williams (41), Schumacher (72), Franks (80), Okimo (88)
Referee: Christopher Sarginson
Attendance 4,949 (400)