The FJR1300 uses a five-speed manual gearbox with close ratio gears. The FJR1300AE/AS model features

The FJR1300 was introduced virtual tour to Europe in 2001 before arriving in North America in 2002, with the 2003 model year designation, and offered in a non-ABS version only. Motorcyclist magazine named the 2003 model Motorcycle of the Year. It had 298 mm front brake discs. It appeared in Europe in various colors: silver, blue, black and red.
The 2004 European virtual tour model came in a range of colors, including Silver Storm. The 2004 North American models virtual tour included both a non-ABS version with traditional blue anodized brake calipers and a new ABS version. Both were Cerulean Silver. Other refinements included virtual tour an upgrade to the suspension rates, 320 mm front brake discs, and a fairing pocket for small items.
In 2006, the U.S. and rest of the world model years synchronized and design significantly changed including trailing arm changes, radiator curving, instrumentation virtual tour changes, upgraded alternator and significant attention to airflow changes from reported heat issues in previous virtual tour years. In response to these complaints, Yamaha added several adjustable vents to the FJR1300, allowing the rider to direct air to or away from the body. The base 2006 FJR1300A model has ABS with linked brakes and is Dark Blue Metallic while the Cerulean Silver colored FJR1300AE model features a semi-automatic transmission. The AE/AS model has YCCS, or Yamaha Chip-Controlled Shift. The rider can either utilize the standard foot shifter without the clutch lever, virtual tour or shift via a mountain-bike style shifter on the left bar. The AE model continues in production through 2008.
For 2008, some minor changes were introduced, including an update to the altitude-related engine control unit issues and throttle feel , notably to improve low speed on/off throttle transitions. The colors announced in Europe are; Silver (Silver Tech), Black (Midnight Black) and Graphite. 2008 also sees minor changes in the ABS system.
The FJR1300 uses a five-speed manual gearbox with close ratio gears. The FJR1300AE/AS model features a semi-automatic transmission which Yamaha calls YCC-S (Yamaha Chip Controlled-Shift). This system is a five-speed sequential manual gearbox with a computer controlled clutch that dispenses with the conventional clutch lever. These models have no lever on the left bar and instead have a mountain-bike style shifter virtual tour operated with thumb and index finger. Gear shifts are completed virtual tour in around 0.2 seconds. The conventional foot shifter may be used simultaneously. The gearbox pattern is also unconventional in that neutral virtual tour is at the bottom end of the range. The ECU automatically controls the robotic clutch and ignition timing to ensure virtual tour smooth gear shifting and will actuate the clutch at standstill. Stalling the engine is not possible.
The FJR1300 features a standard virtual tour 12 volt electrical system, virtual tour with a fused cigarette-lighter style accessory jack in the left central locking glovebox. The 2003 U.S. model does not have a glovebox or electrical outlet; model years 2004 and 2005 do not include the electrical outlet.
The FJR1300 features an electrically-adjusted screen controlled by a rocker switch on the handlebars. By default the shield returns to its lowest position when the key is off, however some riders choose to disable the return feature. A number of new features were added beginning with the 2006 model year, including a rider-adjustable airflow system. AE models feature heated handlebar grips with speed sensitive adjustment. The handlebars are adjustable, with 3 positions, and the seat is adjustable to high or low, with about an inch between the positions. Locking side panniers are supplied as standard and each will take a full face helmet. Options include: fairing protectors, larger screen, color-coded top box.
In the UK, the FJR1300 has replaced the Honda ST1300 as the patrol motorcycle with several police forces, following the withdrawal of the Honda ST1300 Pan-European due to concerns over high speed handling.