Watford started impressively and took the lead in the 25th min with a fine solo goal.
Danny Webber took the ball past two defenders, exchange passes with Johnnie Jackson and beat two more before sending in a cross shot. Gillingham defender Barry Ashby attempted to cut it out but only succeeded in sliding the ball into the net.
Paul Devlin and Neal Ardley both went close as Watford dictated the play with some imaginative football.
Early in the second half, Ardley's shot was off the line and Jay Demerit saw his attempt well saved by Jason Brown.
But gradually Gillingham took over and were particularly unlucky when skipper Paul Smith fired in a rising drive that came back off the woodwork.
Then Darren Byfield shot just wide and Darius Henderson rose to send a header against the bar only for Byfield, following up, to send his shot wide.
Byfield was back again but this time lifted the ball over the bar and the unhappy striker scuffed another attempt wide of the target with only the keeper to beat.
Watford came back with Heidar Helguson going close and Jackson firing a shot just over the bar.
To complete Byfield's misery Paul Jones pulled off a fine scrambling save and Watford was soon scoring their second down the other end.
On-loan midfielder Chris Eagles went past two defenders before cutting a shot back beyond the keeper.