Everton substitute Sean McAllister scored the only goal on 64 minutes, settling a game in which the home side had plenty of attacking possession but without making it count.
The Shrimps made nine changes to the starting XI beaten by AFC Wimbledon at the weekend.
Liam Gibson and Aaron Wildig were the only players to retain their places as Ryan McLaughlin, Scott Wootton and Jacob Mensah all made their first starts.
It also meant a start for Freddie Price, who occupied the central striker’s role in the absence of Cole Stockton.
Everton’s youngsters looked bright in possession early on with wing-back Eli Campbell getting forward to good effect, albeit without the end product to match his approach work.
Morecambe also looked bright down the flanks, especially on the right-hand side where McLaughlin and Wes McDonald showed promising signs.
McDonald cut in and fired over before Callum Jones saw a shot from distance easily gathered by Everton keeper Zan Luk Leban.
Josh McPake spun away from his man and advanced to the edge of the area, only to fire well off target, as did Price when the ball dropped to him 15 yards out.
For their part, Everton gave as good as they got though Letheren was similarly untroubled.
The closest they came was midway through the half when Stan Mills cut the ball back from the right-hand side and Tom Cannon’s first-time shot was a yard or so off target.
Charlie Whitaker sent a free-kick over the bar from 25 yards before the first half drew to a close.
The second half was a much more entertaining affair as McPake, in particular, looked to stake a claim for a starting role on Saturday.
One early effort went straight at Luk Leban as the Rangers loanee looked to run at the Everton backline at every opportunity.
Wootton headed an Alfie McCalmont corner off target and Gibson diverted a McDonald cross wide as the Shrimps had the better of the play.
Nevertheless, it was the visitors who took the lead on 64 minutes moments after Gibson’s effort.
The ball was worked inside from the left to McAllister, who left Letheren rooted to the spot with a fierce effort from the edge of the area.
Another strong run from McPake almost led to an equaliser with 19 minutes left but Luk Leban got down well to turn behind McCalmont’s shot.
Arthur Gnahoua fired over from a tight angle and prodded another effort wide in added time but that was as near as the Shrimps got to getting back on terms and forcing penalties.
Morecambe: Letheren, McLaughlin (Cooney 61), Wootton, Mensah, Gibson, McCalmont, Jones (McLoughlin 82), Wildig, McPake, F Price (Gnahoua 72), McDonald. Subs not used: Andresson, Leigh, O’Connor, Delaney.
Everton U21: Luk Leban, Astley, Campbell, Welch, Mills, Butterfield, I Price, Whitaker, Anderson, Dobbin (McAllister 57), Cannon (Warrington 82). Subs not used: Barrett, Hunt, Hughes, Hagan, Kristensen.
Referee: Andy Haines.
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