Eric Kinder's young side were no match against a lively Harrogate side that ran out comfortable winners.
John O'Sullivan tested the Town 'keeper early on with a drive from distance but it was the home team who broke the deadlock on 18 minutes, Ashley Worsfold finishing a well worked move.
A second goal for Worsfold soon followed, the striker collecting a through ball before firing home despite pressure from Ryan Edwards.
Harrogate almost made it three before the break but Matty Urwin pulled off a great point-blank save to deny Chris Hall.
Kinder rang the changes at the break but it was two who were on from the start, John O'Sullivan and Patrick Antelmi, who went close to reducing the deficit early in the second half.
However, it was Town who increased their lead further when a Rovers clearance fell perfectly for Adam Nowakowski and he hit a 30-yard stunner beyond substitute 'keeper David Raya.
The Under-21s are back in action this Friday evening at Bamber Bridge, kick-off 7.30pm.