2002 model

2003 model
This year the bike got refinements for fairing and windscreen. The flashers were now integrated in the fairing and a small storage box was added to it.
Also the brake system was updated with bigger front disks and the introduction of a version with ABS, the FJR1300A.

2004 model

2005 model

2006 model
The bike got new bodywork and a new ABS, incorporating a combination brake system, as standard equipment.
Also the sidecases are fitted as standard equipment from now on.
The new fairing has an adjustable section at the knee area and a wider range of adjustment for the windscreen. The heat insulation for the rider (regarding engine heat) is improved. The engine is adjusted to meet EU3 regulations and also features a longer gear ratio for lower rpm at cruising speeds.

This year also marked the launch of a new FJR variation model: the FJR1300AS with automatic clutch.
The Yamaha Chip Controlled Shift system allows clutchless gear changes, making it the world's first semi-automatic sports tourer.
Shifting can be done traditionally by the foot lever but also by finger-operated shifters on the handlebar. When operating these, the YCC-S system automatically disengages the clutch and actuates the gear shift in a fraction of a second!
On starting from standstill, the system works as an automatic clutch: On opening the throttle, engine rpm increases and the clutch starts to engage smoothly and automatically.

Detail changes for 2006:
• Longer rear swing arm: to improve high speed stability
• New instrument panel with gear indicator und other features
• Adjustable rider seat (2 positions)
• Adjustable handlebar (3 positions)
• Windscreen not only wider adjustment range but also bigger and wider
• Curved radiator for improved cooling
• New headlight with easy beam adjustment (for tandem riding)
• Ventilation duct under the windscreen to reduce turbulence
• Lockable glove box with DC power outlet
• New position for rear footrest to improve passenger comfort
• New rear mirrors , foldable (for parking) with separate mirror alignment
• Progressive throttle for better responsiveness (eventually changed to normal responsiveness in 2008).

2007 model

2008 model
 

2009 model 
The standard FJR1300A gets an improved clutch with lighter feel and the AS model gets an updated mapping of the control system of the YCC-S, for improved ride quality especially in stop/start urban situations.

2010 model