With McGraw remaining in Baltimore, Hanlon named Kelley team captain. The Superbas won the NL pennant in 1899 and 1900, as Kelley finished tenth in RBI (93), OBP (.410), and tied several players for tenth in home runs (6) in 1899 and led the team with a .319 batting average in 1900, while finishing fourth in the league in SLG (.485), tying Hickman for seventh in RBI (91), and tying Jimmy Collins and Buck Freeman for tenth in home runs (6).