The 25-year-old scored five goals in 15 appearances for the Loftus Road side last season but finished the campaign on loan at MK Dons.
Former Arsenal trainee Emmanuel-Thomas has previously had spells at Ipswich and Bristol City and spent time on loan at Blackpool, Doncaster and Cardiff.
He becomes Gillingham's eighth signing of the summer transfer window.
Find all the latest football transfers on our dedicated page.
League One side Gillingham have signed Queens Park Rangers forward Jay Emmanuel-Thomas on a season-long loan.