Goals from Scott Cuthbert and Jobi McAnuff were the difference in the encounter at Glanford Park, with Matt Sparrow scoring for United.
It was the visitors that started the game the better and they had the first chance when Jobi McAnuff’s diagonal cross from the right found Darius Henderson at the far post but he couldn’t get a clean connection on his header.
The next chance saw the first goal of the game, with it barely being two minutes old when Dean Cox whipped in a corner and Cuthbert rose to head past Olejnik and give Leyton Orient the lead.
Orient took command after the goal and United were struggling to get a foot hold in the game and get any time on the ball through Orient’s quick pressing.
The visitors then had a chance to double their lead when Elliott Omozusi smashed the ball across goal but the ball hit Chris Dagnall and bounced out of play.
United had their first real chance of the game in the 12th minute when the ball was deflected to Gary McSheffrey out on the left but his low drive was just wide of the near post.
Orient’s next opportunity came when a good move down the Iron left saw McAnuff’s looping cross find Dagnall at the far post but his header was gathered comfortably by Bobby Olejnik.
Lyle Taylor was the next to have an opportunity for United in the 28th minute but his snapshot was well over the bar.
The visitors were still looking dangerous and they looked like they might score again when a counter attack saw McAnuff running at the defence and making his way into the box but his shot was straight at Olejnik.
The Iron then started to look a little more like it going forward, with Taylor first having his header well saved by Woods in the Orient goal.
That was then swiftly followed by the ball finding its way to Paddy Madden at the far post but his improvised scissor kick was narrowly wide.
Another quick break from Orient following a cleared Iron corner saw McAnuff with space out wide but his cross was well cleared by O’Neill with Dagnall lurking just behind him.
A long range effort from Shane Lowry was the next opportunity but it was never troubling Olejnik and was well over the bar.
Orient had another opportunity when a mistake from Canavan saw Dagnall looking like he was going to be clean through on the goal but the Irishman recovered with a terrific tackle to stop him from getting a shot away.
That was the last real action of the half, with the visitors deservedly in front at the break and The Iron were going to need a response if they were to pick up any points.
However, it was again the visitors that started the better and McAnuff’s side footed effort was deflected narrowly wide of the post just after half time.
That seemed to act as wake up call for the Iron and they went up the other end and got an equaliser just a minute later through Matt Sparrow.
Gary McSheffrey’s high looping cross from the left stayed in play and found Hawkridge, who hooked the ball back to Matt Sparrow, who expertly volleyed the ball into the bottom corner.
However, that excitement was very short lived when McAnuff restored Orient’s lead just a minute later.
A scramble in the box saw the ball finds its way McAnuff all on his own and he side footed into an empty net to restore the visitors advantage.
Dean Cox was the next to try his luck, with his powerful long range shot forcing Olejnik to push the ball out for a corner.
The game was getting more and more stretched and Chris Dagnall then had an opportunity to make it 3-1 but his shot was well saved by Olejnik.
There was then some controversy when Paddy Madden took the ball past Cuthbert and was through on goal before the referee stopped the game due to an injury to Lyle Taylor.
Orient looked likely again when Henderson and Dagnall linked up well to put the ex-Iron man through on goal but his first touch was lacking and the ball bounced through to Olejnik.
The Iron’s best chance to equalise came when Madden’s dink over the top found Adelakun running towards goal and his cross found Sparrow at the far post but his shot was deflected and cleared.
United were nearly the architects of their own downfall after that when a poor free kick was cleared and saw Dagnall but Myrie-Williams used his pace to get in front of Dagnall and get the ball back to Olejnik.
The Iron huffed and puffed but there were no more clear cut opportunities, with Hakeeb Adelakun’s long range shot wide being the only chance of note and it means that the Iron now head to Oldham to try and bounce back next Saturday.
Scunthorpe United: Olejnik, O’Neill, Canavan, Llera, Williams, Hawkridge (Myrie-Williams, 74), Sparrow, McAllister (Kee, 77, McSheffrey, Taylor (Adelakun, 67), Madden
Unused substitutes: Weaver, Dawson, Boyce, Sutton.
Leyton Orient: Woods, Omozusi, Vincelot, Cuthbert, Cox, James, McAnuff (Petrasso, 72), Lowry, Clarke (Batt, 82 ), Dagnall (Simpson, 75), Henderson
Unused substitutes: Grainger, Baudry, Mooney, Pritchard.
Attendance: 3,264 (261 away).