Clarke moved to New Mexico in his early childhood and was raised in Indian territory, and studied civil engineering in Santa Fe at Brothers College. He began his professional career in 1889 for a minor league team, and made his debut for the Orioles on May 1, 1893. He claims his nickname, "Boileryard", was given to him because of his voice.
During his major league career, he assisted the Princeton University baseball team as a coach. He was in this capacity from 1897 to 1901. He returned in 1909, approximately four years after his retirement from baseball, and stayed until 1927. He came out of retirement again to be an assistant coach for Princeton in 1934, and in 1936 was named manager of the team, and stayed in the position until 1944, when retired again, this time at the age of 75.Bill Clarke Field, the home of Princeton baseball since 1961, is named for Clarke.