In his MLB career, Kelley played in the National League (NL) for the Boston Beaneaters (1891), Pittsburgh Pirates (1892), Baltimore Orioles (1892–1898), and Brooklyn Superbas (1899–1901), before he jumped to the upstart American League to play for the Baltimore Orioles (1902). He returned to the NL with Cincinnati Reds (1902–1906) and Boston Doves (1908). Kelley served as player-manager of the Reds (1902–1905) and Doves (1908). After extending his career in the minor leagues, he coached the Brooklyn Robins (1926), and scouted for the New York Yankees (1915–1916).