City fired in two early goals and could have had more before the visitors got into the game.
The Gills went on to dominate the second half, but despite plenty of possession failed to force a single save out of home keeper Rob Burch.
Lincoln threatened right from the first minute with Lee Frecklington and Adrian Patulea linking well, but skipper Scott Kerr failed to get in his cross.
City went in front with a simple goal after 12 minutes. Paul Green sent over a cross from the right and Frecklington lost his marker to head home at the near post.
Gillingham were still reeling and six minutes later fell further behind.
An excellent flick on from Adrian Patulea set Dany N'Guessan free. The Frenchman ran 30 yards at the Gills defence, before finishing with a superb shot into the top corner with keeper Simon Royce left helpless.
Lincoln kept up the pressure and after Janos Kovacs headed over the Imps should have increased their lead on 23 minutes.
Frecklington picked up a poor Gillingham pass and found Patulea but from a good position the striker failed to find the target.
Patulea was involved again on the 31st minute when he fired a cross from the left into the box. Lenell John-Lewis got in front of the Gillingham defence but saw his header fly narrowly over.
Gillingham began to push forward towards the end of the first half and Adam Miller should have done better with a long-range effort which went over.
Nicky Southall then caused problems for Lincoln with a deep cross which was headed down by Mark McCammon, but City keeper Burch was alert to save.
The Gills had all the possession in the second half as Lincoln tired badly.
But the visitors struggled to create chances and always looked vulnerable to the counter attack. Stefan Oakes sent Patulea clear in the 56th minute only for the striker to fire wide.
Oakes was the creator again six minutes later when his cross picked out Lee Beevers, but the big centre-back headed well over from six yards out.
Gillingham looked more dangerous after substitute Albert Jarrett replaced the injured McCammon, but still they made little impression on the Lincoln defence in which Kovacs was outstanding.