On the inside of the car, the EX trim received upgrades which includes steering wheel mounted redundant audio controls and an outside temperature monitor. The stereo system was also XM Satellite Radio ready. All CR-Vs also had revised rear seat headrests, which have been redesigned to reduce rear view blockage.

Mechanically, the 2005 was also changed. A major change included a drive-by-wire throttle for all CR-Vs. The RT4WD system was improved; it had been tuned to activate faster in low traction situations. Also, the automatic transmission for the CR-V now had one extra gear (total of 5), for improved highway fuel efficiency.

In the United States, in accordance with Honda's Safety for Everyone campaign, every 2005 CR-V and onwards have ABS, front airbags, side airbags for front passengers, and side-curtain airbags with rollover sensors for all outboard occupants. Also, Electronic Brake Distribution and Vehicle Stability Assist have been added and are standard equipment on all trim levels. CR-Vs in other countries such as Australia continue with only dual airbags and ABS as standard equipment. Side airbags are optional, while curtain airbags are unavailable.

Following the tradition of adding a trim level above the EX during the refresh like the first generation CR-V, Honda added the SE trim level for the 2005 CR-V. The CR-V SE has painted bumpers, body side molding, and spare tire cover. For a more luxurious experience, Honda added a leather interior, leather steering wheel, heated side mirrors, and heated front seats. A new color, Pewter Pearl, can only be found on the SE. The SE also includes a hard body coloured cover for the spare tire on the back.

For the 2006 model year, two new colors have been added, Royal Blue Pearl and Alabaster Silver Metallic. These colors are available on the CR-V LX and EX only.