In 2003, Kanaan drove for Andretti Green Racing in the No. 11 7-Eleven-sponsored Dallara IR03-Ilmor-Honda Indy V8 HI3R. Kanaan got consecutive pole positions at the Toyota Indy 300 at Homestead-Miami Speedway, finishing fourth, and the Purex Dial Indy 200 at Phoenix International Raceway, where he would go on to win his second Indy car race after leading for 79 laps. Kanaan then led the point standings after Phoenix. At the Indy Japan 300 at Twin Ring Motegi Kanaan was involved in a crash with Scott Dixon on lap 178 and finished 14th. There was a question whether Kanaan would be able to compete in the Indianapolis 500. Kanaan was able to participate and qualified 2nd and led for two laps, eventually finishing 3rd behind countrymen and Marlboro Team Penske teammates Gil de Ferran and Hélio Castroneves. Kanaan regained the points lead and held on for the next eight races, with the exception of the Belterra Casino Indy 300 at Kentucky Speedway where he dropped to second-place, based on consistent finishes. Following an 18th-place finish at the Firestone Indy 225 at Nazareth Speedway Kanaan dropped to 3rd in points. Kanaan entered the season-ending Chevy 500 at Texas Motor Speedway third in points and was involved in a five-way battle for the championship with de Ferran, Dixon, Castroneves and Sam Hornish, Jr.. In the race, Kanaan started ninth and led for 52 laps, only to finish two laps down in 14th place. Kanaan finished fourth in points behind Dixon, de Ferran, and Castroneves with 476 points.