Making the short trip to Playing Fields, Terry Moore’s side targeted a repeat performance from the First Round.
Facing Bishop Sutton at the start of October the Young Glovers ran out 4-0 victors to set up the Second Round tie with Shepton.
Unable to call upon a host of players due to injury and first-team involvement, a number of Under-16s featured in the cup clash.
After a well-battled opening half an hour, Town fell behind on 36 minutes as the break approached.
Kailan Gould, who had threatened before, lobbed a shot over Kacper Kowalczyk to give the hosts the lead at the halfway stage.
Needing a bright start to the second half the green and whites were dealt a blow seven minutes after the restart when Francois Callen doubled Shepton Mallet’s lead with a neat finish.
Continuing to search for a way back into the match the Glovers produced some neat play against their senior opponents, but committing numbers forward Mallet added a third late on through James Billing to round off the scoring.
Now looking to continue their impressive EFL Youth Alliance campaign, the Under-18s host Exeter City on Saturday (11am) at Huish Park with supporters encouraged to back the Young Glovers.