Major changes to the bike were made during in the 1999, when Honda changed to fuel injection. The CBR featured a six speed transmission gearbox, with an electric start, a Linked Braking System, with a 256 mm single disk with three-piston caliper. The wheels of the bike had a holo section triple spoke cast. Later on in 2001 the motorbike also received an LCD instrument cluster.

Many colors have also been introduced in the CBR, and changes to the exhaust system and the fuelling system shave also been improved to make the consumption more effective and efficient. A new dashboard was also introduced along with a digital speedometer, which was placed in the centre of the dashboard.

No significant changes were made during the years, except for the color selection but In 2005 Honda changed the bikes fuel tank capacity to twenty three liters, whereas later on in 2007 the bike was introduced with ABS braking system.