Orient raced into a two-goal lead after 21 minutes, with the hosts maintaining their lead going in at the break.
On the hour-mark the Town pulled one back after Tra Lucas beat his defender and saw his low ball across the six-yard area diverted into the back of the net by an Orient player.
Wilson then got his side back on level terms with four minutes to go as his left footed volley went through the keeper’s hands, ensuring the Hatters got a share of the spoils.
The result moves the Town up to fifth, with their next game against Stevenage this Saturday.
For the full table, click here for the EFL Youth Alliance Newsletter.
Town team: Horlick, Francis, Bateson, Wedd, Nicolson, Kalonda, Beckwith (c), Pettit, Boorn, Stevens, Lucas.
Subs: Bentley, Wilson, Swan, Newton, McJannet.