Exeter dominated the first half and created a host of chances to go in front. The best of those fell to Jamie Cureton, Exeter's 20-goal top scorer, who could easily have had a hat-trick.
Twice he got on the end of balls from Craig Woodman but failed to find the net. His best chance came when he was found by Matt Oakley 18 yards out, only to scuff the ball over the crossbar.
Gillingham had created little in the first half and they were not much better after the break.
Scot Bennett struck a fierce shot straight at Stuart Nelson for Exeter and substitute Guillem Bauza dragged an effort wide of the far post from 18 yards.
Gillingham's only opening in the second half came from substitute Danny Kedwell, but he hooked a shot wide.