The Os took the lead with just five minutes on the clock when David Mooney picked up John Lundstram's pass inside the box and found the bottom corner.
Mooney turned provider for Orient's second, lining up Dean Cox for a shot from outside just the area before the midfielder beat Gills goalkeeper Stuart Nelson with a thunderous strike.
Gillingham almost pulled one back before the half-hour mark, Amine Linganzi finding space in the box and letting fly, only to be denied by the outstretching Jamie Jones.
However, two goals in one minute before the stroke of half time made it mission impossible for them, as Kevin Lisbie headed a third before Mooney made it 4-0 at the interval with his second of the afternoon.
Mooney was denied his hattrick early in the second period as Nelson got down quickly to keep out the striker's effort at close range, but it was an otherwise sedate opening to half.
There were chances at both ends as the clock ticked on, Adam Barrett coming within inches of heading a consolation for the Gills, before Lisbie forced Nelson into action again.
Orient netted their elusive fifth in the 78th minute as Chris Dagnall turned in Lisbie's low cross from close range, but the visitors added a modicum of respectability to the scoreline with a late consolation.
Craig Fagan rifled home Joe Martin's delivery with eight minutes left to play for a final scoreline of 5-1.