After going into the half time break 1-0 down, goals from Sam Dalby, Ruel Sotiriou and Toby Stevenson gave the O’s the lead and was enough to secure the victory.
Youth Team Coach Danny Webb made one change to the starting XI with Hector Kyprianou replacing Mikhail Hemans.
The O’s looked the brightest of the two teams from beginning to end, and created two chances in the early stages.
The first coming through Sotiriou, who latched on to the edge of Arthur Janata’s early kick, the striker controlled and turned his man before his shot rolled wide of the target.
The second chance came through Dalby, who received a through ball from Amin Benyoucef but was brought down in the box before he could get a shot away and the ref waved away the penalty appeals.
Against the run of play, Ben Wilmot opened the scoring for Stevenage by connecting with a free-kick from the wide right.
With 25 minutes until the break, the O’s continued to look the strongest of the two teams despite being a goal down but were unable to make the most of their possession.
Teddy Perkins released Sotiriou with a long ball over the top and the latter was one-on-one with the ‘keeper who managed to save the strikers first-time effort.
Again, Sotiriou got in behind the defence after high pressure forced an error, but the resulting effort rolled just wide and saw the O’s go into the break a goal behind the hosts.
Within minutes of the restart, Orient found themselves deservedly level when a long range free-kick was floated into the box and met by the head of Toby Stevenson whose cushioned header allowed Dalby to strike the ball home on the turn from close range.
It was 2-1 to the O’s soon after, as another long ball forward from Andrew Camilo-Tayaca freed Sotiriou who lost two of his markers brilliantly before slotting the ball into the corner of the net to claim his first of the season.
Five minutes later, the O’s won a free-kick from 25-yards out and Dalby struck the bar with a spectacular effort but Stevenson was quickest to react and nodded in the rebound to make it 3-1.
The O’s were still on the hunt for more, but Dalby’s goalbound header had beat the ‘keeper but not the man on the post.
The O’s youngsters showed good discipline throughout the closing stages and saw out the rest of the game comfortably and now await their next opponents in the third round of the cup.
ORIENT: Arthur Janata, Andrew Camilo-Tayaca, Teddy Perkins (C), Toby Stevenson, Alfie Fleming, Ernold Haxhiu, Amin Benyoucef, Charles Clayden (Luca Carter-Henry), Hector Kyprianou, Ruel Sotiriou (Wynford Marfo), Sam Dalby
GOALS: Dalby, Sotiriou, Stevenson