For 2009, Kawasaki released an updated Ninja 650R which includes new bodywork, mirrors, gauges, lighting, and a new tune on the same 649 cc (39.6 cu in) engine.

Along with chassis and minor tweaks, an all-new bodywork design was introduced to the 2012 Ninja 650 and ER-6n along with a new 2-piece seat assembly, 20mm wider handlebars, and a new tachometer above an LCD display that shows speed, trip meters, fuel consumption, etc.

The new Ninja 650 also comes equipped with an Economical Riding Indicator which activates when the bike is consuming low amounts of fuel.

For 2017 Kawasaki has updated the Ninja 650 with a new trellis style frame adding to the new lighter weight and better handling.

With new sharper styling it has done away with the distinctive side mount rear shock for a more conventional one, it has also added a slipper clutch.