From 2021, production availability is limited to a non-homologated race-only specification in most global markets,[2][3] causing race organisers to realign their engine eligibility criteria to encourage other manufacturers having larger than 600 cc displacements to enter road-race competition from 2022.

The 2006 model year was a significant upgrade with a new engine-management system featuring the YCC-T ride by wire throttle and a multiplate slipper clutch.

[7] The 2008 model incorporated the YCC-I variable-length intake system to optimize power at high engine speeds, a slight change in exterior bodywork for better aerodynamics, and an improved Deltabox frame design.

[10] In February 2006, Yamaha admitted the bike's true engine redline was more than 1,000 rpm lower than what was indicated on the tachometer and had been advertised,[11] and offered to buy back any R6 if the customer was unhappy.

[16] Chaz Davies helped Yamaha to win both the riders and manufacturers title during the 2011 Supersport World Championship season.