In 2006, Yamaha released the FJR 1300AE version that introduced several upgrades for enhanced comfort for the rider and passenger while still maintaining its performance characteristics of a sports machine.
First ao all, Yamaha introduced on the 2006 AE model the electronically controlled clutch system that made life easier for the rider with its still manual-operated shifter that didn't require clutch assistance at shifting gears, which resulted in a clutchless handlebar.
The sharper-looking bodywork and air-management system kept the rider much cooler, with a central vent located under the instrument panel that reduced negative pressure and also packed adjustable side panels that allowed the rider to direct the airflow.
In addition, the model featured a new, curved radiator, a longer swingarm that offered better riding and handling characteristics, an adjustable windscreen, a newly designed rear frame with an integrated grab handle, repositioned footpegs for more comfort, a lockable glove compartment, and integrated turn signals for a cleaner look.
In the performance department, the 2006 Yamaha FJR 1300AE remained unchanged with its 1,298cc four-stroke four-cylinder liquid-cooled engine that delivered an output power of 145 hp with a peak at 8,500 rpm and 125 Nm (99 lb-ft) of torque at 6,000 rpm.
The big sport-touring machine, with its electronically controlled clutch system and five-speed transmission, reached a top speed of 245 kph (152 mph).