In 2006, Honda decided to make a number of changes to its 2006 S2000. First and foremost, the vehicle was upgraded with a new Drive-By-Wire throttle control system which allows the engine management computer to make minute, continuous throttle adjustments to maximize throttle response based on driving conditions. The Drive-By-Wire system also makes the cruise control more precise.
Another driver aid added to the 2006 S2000 is Honda's new Vehicle Stability Assist system, which made the vehicle more stable in low-traction situations and more controllable in high-performance situations. The system constantly monitors turning rate, steering and throttle input, and braking pressure to determine if the car is following the driver's intended path. If it is not, the system can apply any, some, or all of the four disk brakes, as well as alter throttle position, to bring the vehicle back into line. The system can be switched off for spirited and/or tail-out driving.
Cosmetic changes for the 2006 S2000 include a new seat design and an updated center console. The 2006 S2000 also includes a "maintenance minder" system which alerts the driver when scheduled maintenance is required. Outside, the car recieved a new color in its palette, Laguna Blue Pearl, which is available with a black leather interior. The 2006 S2000 also recieved new 17" alloy wheels.