Blackpool were denied their first home league win of the season by a superb goalkeeping performance from Gillingham's Darren Randolph.
Gillingham scored in the third minute when Guylain Ndumbu-Nsungu tapped in as the hosts' defence hesitated.
Randolph could do nothing about Blackpool's equaliser, a Scott Vernon header from Wesley Hoolahan's cross.
But the 19-year-old stopper, on loan from Charlton, made a series of superb saves as Blackpool went for the win.
Blackpool: Evans, Barker, Evatt, Jackson (Bean 60), Coid, Forbes, Southern, Gillett, Hoolahan (Joseph 71), Morrell (Parker 60), Vernon.
Subs Not Used: Edge, Graham.
Goals: Vernon 35.
Gillingham: Randolph, Jupp, Sancho, Cox, Johnson, Flynn, Pouton (Spiller 81), Crofts, Jackman, Jarvis, Ndumbu-Nsungu (Mulligan 90).
Subs Not Used: Easton, McDonald, Clohessy.
Goals: Ndumbu-Nsungu 3.
Ref: M Pike (Cumbria).