Colchester U23s 1 Newcastle U23s 2
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Magpies beat Colchester in Premier League Cup
Wednesday's 6-3 win against Swansea saw Tom Heardman score four times, but this time Charman was the main man with a goal in each half against Colchester United.
And three more points leave Peter Beardsley's side in a strong position, with two wins from three Group D matches so far.
The home side included first-team regular Kurtis Guthrie on his return from injury and the well-travelled frontman had the game's first opening, seeing a shot saved by Nathan Harker before Courtney Senior fired over the bar soon afterwards.
In the tenth minute, Newcastle thought they had taken the lead when Daniel Barlaser bundled the ball home, but he was adjudged to have used his hand to beat goalkeeper Dillon Barnes.
After a Callum Roberts free-kick whistled just wide, United had the ball in the net again through Kyle Cameron, but this time the flag went up for offside - and then Barlaser saw another effort chalked off for the same reason.
In an end-to-end first half, Harker denied Louis Dunne, then Wales youth international Charley Edge saw a free kick cannon back off the crossbar.
And on the stroke of half time, Beardsley's side took the lead through Durham-born Charman's clinical strike.
Two minutes into the second half, Colchester equalised when Tariq Issa's shot squirmed past Harker.
But Newcastle went back in front in the 66th minute through Charman, who found the bottom corner after a swift counter-attack.
Eoin McKeown came close to another leveller for the home side, then Senior saw a shot deflected wide before Edge curled an effort just over.
The Magpies almost added to their lead when substitute Mackenzie Heaney clipped the woodwork late on, but were grateful to Harker for a fine stoppage time save from Harker to keep out Diaz Wright's volley.
In addition to a hard-earned victory and Charman's brace, Beardsley will have been hearted by the return from injury of Michael Newberry, who played for 65 minutes in his first start of the season.
United are back in Premier League 2 action on Friday, when they entertain West Brom at Whitley Park (kick-off 7pm UK time).
Newcastle United Under-23s: Nathan Harker, Michael Newberry (Ben Kitchen 65), Kyle Cameron, Owen Bailey, Josef Yarney, Macaulay Gillesphey, Yasin Ben El-Mhanni (Callum Smith 81), Daniel Barlaser, Luke Charman, Dan Ward (Mackenzie Heaney 78), Callum Roberts
Subs not used: Paul Woolston, Lewis McNall