Another clean sheet and an all-important goal from Stuart Dallas gave Town a vital three points that saw them lifted off the foot of the Football League.
They now have a break from league action and face a very tough test against a Mariners side who lie in the play-off places in the Conference and defeated League Two opposition in the shape of Scunthorpe United in the last round.
Boothroyd is hopeful that striker Roy O'Donovan will make his return from injury in the game although Izale McLeod is cup-tied having played and scored for MK Dons in the 1st Round.
Grimsby have another fixture before the Northampton match after an FA Trophy draw against Coalville at the weekend but will be without striker Liam Hearn for some time. Scans on the 28-year-old's knee after the recent game against Barnet have uncovered a serious cruciate injury.