It was a deserved win for the U's at the JobServe Community Stadium but the U's had to be patient to make the breakthrough, with Fulham goalkeeper Alfie McNally in fine form.
Colchester boss Danny Cowley, who watched the game from high in the West Stand, made nine changes to his starting line-up for their final Vertu Trophy group game, against Hayden Mullins’ Fulham under-21 side.
Teddy Bishop and Kyreece Lisbie were the only players to retain their places in the side following last weekend’s defeat to Bromley, with Cowley giving some of his other players a chance to shine.
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Will Goodwin made his first start since the opening day of the season, while midfielder Milton Oni was in the U’s first-team starting line-up for the first time since suffering a serious knee injury in August, 2024.
Captain Tom Flanagan returned from injury to take his place at the heart of the U’s defence while the likes of Sam Kuffour Jnr, Josh Powell and John-Kymani Gordon also got the chance to impress and Kaion Lisbie was among the substitutes, after being included in the Colchester first-team squad for the first time.
Cowley had said prior to the game that it was a chance for players to stake their claim for a place in his starting line-up and Colchester started brightly.
Rob Hunt _(Image: Steve Brading)_
They were almost ahead in the 11th minute when Fulham goalkeeper Alfie McNally made a super save to deny Goodwin's first-time effort from point-blank range, after Kyreece Lisbie had beaten Brad De Jesus down the right and delivered a low cross into the six-yard box.
Colchester went close again soon after when Flanagan's goalbound volley was blocked in the six-yard box by a Fulham defender while only a tidy piece of defending prevented John Kymani Gordon from getting on the end of Lisbie’s dangerous low cross at the far post, following Oni's brilliant run and pass.
Colchester dominated the possession and went close again four minutes before the break when Jaden Williams' header was well saved at close range by Mcnally after Sam Kuffour Jnr had helped on Powell's corner.
Nicky Cowley _(Image: Steve Brading)_
But the sides went in level at the break and Colchester were made to work hard in their quest to make a breakthrough, by the Premier League side's talented youngsters.
Goodwin fired wide first time from a quickly-taken corner from half-time substitute Arthur Read before Colchester were presented with a golden opportunity to take the lead in the 57th minute when they were awarded a penalty, after Alfie White was adjudged to have fouled Gordon in the box, following Read's corner.
Chance - Jaden Williams sees his penalty saved by Fulham U21 keeper Logan Cook _(Image: Steve Brading)_
But Williams' penalty was saved low to his right by Mcnally and the chance went begging.
Kaion Lisbie was sent on for his professional debut for Colchester just after the hour mark after replacing his brother Kyreece and Samson Tovide was also introduced, as the U's searched for a winner.
Colchester dominated proceedings in the second half and Read turned his marker well before driving a low shot wide of the far post with 20 minutes remaining.
Kyreece Lisbie _(Image: Steve Brading)_
And Read went close again soon after with a low effort from the edge of the area that was well saved by McNally, after Tovide had laid the ball into his path.
Colchester had a penalty appeal rejected after Williams was sent flying by the on-rushing McNally in the area before the hosts finally made the breakthrough, in the 80th minute.
After good play by Oni and Rob Hunt in the build up, Tovide struck a superb shot into the far corner past the despairing McNally, to give the U's a deserved lead.
Gordon's curled effort was brilliantly tipped over the bar by McNally before substitute Jack Tucker doubled Colchester's lead in the 88th minute when he nodded home Read's corner.
**MATCH STATS: Colchester United:** Smith, Hunt, Kuffour Jnr, Flanagan (sub Tucker, 68), Powell, Bishop (sub Read, 46), Oni, Gordon, Kyreece Lisbie (sub Kaion Lisbie, 63), Williams, Goodwin (sub Tovide, 63).
**Substitutes (not used):** Vincent-Young, Harvey, Chamberlain.
**Fulham under-21s:** McNally, Cook, Gofford, Loupalo-Bi, Jesus, Nwoko, Olyott (sub Benchaita, 84), Quashie, Wahid (sub Cavell, 90), White, Adams Zepa.
**Substitutes (not used):** Mayer, Dair, Gomins, Hamilton Khan, Schutter.
**Referee:** Isaac Searle.
**Goals:** Colchester: Tovide (80), Tucker (88).
**Bookings:** Colchester: Goodwin (unsporting behaviour, 44), Flanagan (foul, 59). Fulham: White (foul, 57).
**Sending off:** None.
**Attendance:** 1,061 (52 Fulham U21 fans)