Hatters fell behind midway through the first half, but were level thanks to striker Jemale McKenzie-Lowe’s tidy finish just before the interval.
In the second period, Hatters had a goal ruled out for offside, before the Bees netted three times to condemn Town to only their second league defeat of the season.
U18s boss Paul Driver said: “We had two or three chances to move in front in the second half, but didn’t take them.
“We got punished on the break for it and went on to lose 4-1, which was very disappointing.”
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Hatters: King, Hawkes, Perry, Oakley (Justin 85), Chabata, Tamplin, Ngwala, Trotman, Allman (Amadi 66), McKenzie-Lowe, McMonagle (Tayali 70).
Subs not used: Whybrow, Crilley.