Joe Martin’s 55th-minute goal consigned Wycombe to a 1-0 defeat at Adams Park.
Wanderers were unchanged from Saturday’s victory at York and looked the better side in the first half, but the visitors were much-improved after the break and secured the win despite having Tom Flanagan sent off late on.
Stuart Beavon had Blues’ first effort of the game in the seventh minute when he neatly controlled Sam Wood’s cross, turned and shot goalwards from the edge of the area, only for his strike to deflect off a defender and over the bar.
Danny Kedwell headed wide for the visitors when well-placed and much of the early threat was coming down Gillingham’s right with Myles Weston looking lively.
Wycombe were inches away from taking the lead in the 13th minute when Stuart Lewis surged forward from halfway and found Sam Wood. The winger then curled right-footed towards the bottom corner, but the just the wrong side of the post.
Lee then played a clever ball over the top for Weston and the winger beat Gary Doherty before firing straight at Blues centre-back Leon Johnson when he should have done better.
Weston was causing Wycombe’s defence headaches and he was only denied by a fine Nikki Bull stop following another marauding run in the 20th minute.
Beavon was denied by Stuart Nelson after Matt Spring’s initial effort had fallen to the striker in the area. There looked to be contact from a defender as Beavon collected the ball, but to his credit he stayed on his feet.
Joel Grant then flashed a shot wide of Nelson’s right-hand post before mis-hitting another effort from the edge of the area as the Blues enjoyed a prolonged spell of pressure.
Gillingham keeper Nelson found Spring’s 30-yard free-kick too hot to handle in first-half injury-time, but a defender was on hand to save his blushes and Doherty then headed the resulting corner just wide.
Bull was called into action early in the second half, but he parried Charlie Allen’s effort and the substitute fired the rebound wide. Wycombe’s keeper then had to be alert to tip Tom Flanagan’s header over the bar.
The visitors took the lead in the 55th minute when Weston’s 25-yard free-kick came back off Bull’s left-hand post and fell kindly for Joe Martin who tapped into an empty net from eight yards.
Bull had to be at his best to turn away Whelpdale’s long-ranger, but it was Wycombe who were the next to come close from distance.
Grant picked the ball up on halfway, burst past two defenders and let fly from 25-yards, but Nelson parried the powerful strike and unfortunately for Wanderers the ball fell kindly for a defender to clear.
Blues were handed a lifeline 12 minutes from time when Tom Flanagan fouled Richard Logan midway inside Gillingham’s half and was shown a second yellow card.
Beavon had a strike blocked by Callum Davies and Oli shot over, but Gary Waddock’s side struggled to create openings against the 10-men who held on for the win.
Wycombe: Bull, Stewart, Basey, Doherty (c), Johnson, Spring, Lewis, Bloomfield (Logan 63), Grant, Wood (Oli 43), Beavon.
Subs not used: Harrison, Winfield, Angol, Kewley-Graham, Hause.
Gillingham: Nelson, Fish, Martin, Flanagan, Barrett, Dack (Allen 46), Lee, Payne, Whelpdale (Davies 78), Weston, Kedwell (c) (Jackman 84).
Subs not used: Forecast, Strevens, Frampton, Burton.