Rutto initially began his career in athletics as a steeplechaser. He won the gold medal in the 2000 m steeplechase at the IAAF World Youth Championships and set a world youth best time of 5:30.27, overhauling Soviet runner Mykola Matyushenko's record which had stood unbettered for almost two decades. Rutto demonstrated his ability further with another record run of 5:27.64 in the event two months later in Liège. He ran in the junior race at the 2004 IAAF World Cross Country Championships and finished in seventh place, forming part of the winning Kenyan junior team. He returned to steeplechasing on the track later that season and built upon his youth title with a win at the 2004 World Junior Championships in Athletics, where he achieved a personal best of 8:23.32 for the 3000 m steeplechase. He defeated Musa Amer Obaid with a sprint to the line to continue Kenya's undefeated streak in the competition.