Kelly began his professional career for the Victoria Bees of the Class-B Northwestern League in 1914 and 1915. During the 1915 season, he was purchased by the New York Giants from Victoria for $1,200 (equal to today). The Giants were rebuilding their team, and they saw Kelly as a possible replacement for Fred Merkle. However, he played sparingly for the Giants in his first MLB seasons, appearing in only 17 games in 1915 and 49 games in 1916. He was selected off waivers by the Pittsburgh Pirates on July 25, 1917 to back up Honus Wagner, but did not hit sufficiently. The Pirates waived Kelly, and he was reclaimed by the Giants from the Pirates on August 4, 1917. The Giants optioned Kelly to the Rochester Hustlers of the Class-AA International League, where he played the rest of the 1917 season. Kelly did not play professionally in 1918 due to his military service. The Giants sold Kelly to Rochester before the 1919 season to acquire Earl Smith.