Early in the first half and Hull took the lead following a mishap at the back from Wanderers, allowing Keane Lewis-Potter to smash the ball into the bottom corner past James Aspinall.
Both teams fought it out evenly until the half time break, with neither side able to test one anothers goalkeeper.
Moving into the second half and Joe Pritchard went close with a shot that narrowly went wide after good build up play from David Lee's men.
With eight minutes to play, Wanderers were looking close to finding an equaliser before Shakeel Jones-Griffiths was sent off for a second bookable offence after bringing down Will Keane.
Wanderers kept pushing for that vital goal but ultimately were caught on the counter attack in the latter stages as Keane Lewis-Potter grabbed his second goal of the game.
The U23s now sit fifth in the Professional Development League, only a point off top spot with a game in hand over current first place Birmingham City.
Their next game is at home to the Blues at the County Ground, Leyland on December 17, kick off 7pm.
Wanderers XI: Aspinall, Brockbank, Earing, Zouma, Boon, Ireland (McKenna 60), Connell, Navarro (Broughton 80), Pritchard, Jones-Griffiths, Kelly (Darcy 75)
Unused substitutes: B.Williams, Hartshorne.