He finished 6th at Portland and 7th at Burke Lakefront Airport, where he was battling for 2nd with Mario Domínguez when they collided on the penultimate lap. Dan was again competitive at San Jose, moving up from 9th to 2nd before a gearbox failure put him out at mid-distance. At his next race, in Denver, Clarke moved into 3rd place in the final lap (because of a collision of two drivers ahead of him) to achieve his first podium finish as a Champ Car driver. Indeed, the Denver 3rd place was the first podium finish for a Champ Car Rookie driver in the 2006 racing season.