After an injury to Lee Bullock in the opening two minutes and a low shot from Hayden Coulson that was deflected just wide, it was Whitby who opened the scoring after nine minutes when David McTiernan was set away down the left with a well-placed ball over the top. He squared toDale Hopsonwho drilled home from close range.
Another Whitby change came on 15 minutes when Ben Atkins limped off and just as the first change brought another ex-Boro Academy player in to the fray when Paul Weldon replaced Bullock, so it was this time as Kieran Weledji replaced Atkins.
In patches in the first half it was every bit as tough a game as Boro expected, though they settled to play some nice football and went close through Joao Morelli before equalising on 32 minutes when Harry Chapman capitalised on defensive hesitancy to set up Alex Pattison to drill home and follow up his goal for the first team at Doncaster on Saturday.
A raft of changes came during the break, with several more in the second half as run outs were given to most of the squad.
They benefitted Boro who found their range and racked up the goals.
Joe Wheatleymade it two on the hour with a delightful free-kick curled in from 20 yards; two minutes later Hayden Coulson stroked home from 20 yards to make it three.
Jordan McGheewill never score a more simple goal than the tap in that opened his Boro account on 69, then Callum Cooke stroked home from the edge of the penalty area after Mondal had seen a low shot saved.
A consolation for Whitby came on 90 minutes when Elliott Anderson shot low into the corner from 12 yards.
Boro U23s:Fryer; Johnson (Halliday 46), McGhee, Elsdon (McGoldrick 46), Kitching, Maloney (Wheatley 46), Tavernier (Tinkler 46), Chapman (Mondal 66), Morelli (Fewster 46), Pattison (Kitching 66), Coulson (McAloon 66).