One problem related to check engine light on has been reported for the 2006 Toyota 4Runner. The most recently reported issues are listed below. Please also check out the statistics and reliability analysis of the 2006 Toyota 4Runner based on all problems reported for the 2006 4Runner.
Traction control light came on, check engine light came on and vehicle would move only slowly. Turned car off and on several times, tried engaging 4 wheel drive and other drive functions, tried accelerating, but vehicle would only move slowly. After turning off and on one more time the vehicle drove as normal but all the warning lights stayed on. This happened in a parking lot while going slowly. Mechanic has indicated that this resulted from a failure of the air injection pump and air valve, which apparently for some reason turns off traction control. This is a common enough problem on tundras and sequoias that there is an "extended warranty" offered on these vehicles. I do not know if the air injection pump and air valves on 4 runners are the same design or same model, but there are numerous complaints on the internet of the same problem for 4 runners as for tundras.