Kanaan returned with Andretti Green Racing in the No. 11 7-Eleven-sponsored Dallara IR05-Ilmor-Honda Indy V8 HI4R in 2006. The entire season would be a struggle for the entire Andretti Green team compared to previous seasons due to in part Marlboro Team Penske and Target Chip Ganassi Racing beginning to use Honda engines due to Toyota withdrawing after 2005. Kanaan's only win of the season was at the ABC Supply Company A.J. Foyt 225 at the Milwaukee Mile. Kanaan's best start of the season was a second at the Watkins Glen Indy Grand Prix presented by Tissot at Watkins Glen International. At the Indianapolis 500, Kanaan qualified fifth and in the race led for 12 laps. On lap 190 Felipe Giaffone crashed in turn 2 while Kanaan still had to make his final pit stop; as a result, he pitted under caution and dropped to fourth place. On the final lap of the race, Dan Wheldon passed Kanaan. Kanaan finished in fifth-place behind Sam Hornish, Jr., Marco Andretti, Michael Andretti and Wheldon. On 28 May 2006, Kanaan's friend Rubens Barrichello wore Kanaan's helmet livery during the Formula One Monaco Grand Prix and Kanaan wore Barrichello's helmet during the Indianapolis 500. The two of them created a charity offering financial and technical aid to institutions within the voluntary sector, the Barrichello Kanaan Institute. Kanaan would have an issue with another of his long-time good friends and a former teammate from his time at Tasman Motorsports, Hélio Castroneves. Kanaan and Castroneves had developed an intense rivalry that has resulted in some hard feelings. Castroneves accused Kanaan of costing him the 2006 series championship by racing him too hard for position in the final race. Kanaan countered that he was not paid to let other people pass him for position. The two started to patch up their differences at 2007 Indianapolis 500. Kanaan finished 6th in points 384 points.