He also managed the Chicago White Sox and Boston Red Sox and spent several seasons coaching in collegiate baseball and in the minor leagues. Later in life, he spent many years as a scout for the Red Sox. He was elected to the Baseball Hall of Fame in 1945. He worked for Boston until 1953. He died of heart problems the next year.
Duffy, born in Cranston, Rhode Island, was a textile mill worker who had taken up baseball as a semipro for weekend diversion. He played a couple years of minor league ball in the New England League before jumping to the majors, starting up in the league's initial season of 1886, and playing on clubs in Hartford, Springfield and Salem, as well as the Lowell, Massachusetts team in 1887.
From 1891 through 1900, Duffy knocked in 100 runs or more eight times. In 1894 Duffy had one of the greatest seasons in baseball history, leading the league with 18 home runs, with 145 RBI and a .440 batting average (see Major League Baseball Triple Crown). Duffy's .440 average is the major league single-season batting average record. At one point during the season, Duffy had a 26-game hitting streak. He was player-manager for the Milwaukee Brewers in 1901. During the 1902 and 1903 seasons, Duffy was player-manager for the Western League's Milwaukee franchise.
Duffy was a player-manager for the Phillies from 1904 to 1906. He finished his career in 1906 with 106 home runs which was, at the time, one of the highest career totals.
Duffy spent three years (1907–1909) as manager of the Providence Grays. He made $2,000 in his last season as the Providence manager and The Evening News in Providence wrote that Duffy was paid hundreds of dollars less than any other manager in the Eastern League. During Duffy's three seasons, Providence finished in third place, second place and third place, respectively.
Duffy agreed to manage the Chicago White Sox in 1910. He stayed with the team in 1911. He moved to the Milwaukee Brewers of the American Association in 1912, but he was fired after a season in which the team struggled. He turned down an offer to manage the 1913 St. Paul Saints, saying that he was hoping to work in the east. He coached the Harvard varsity and freshman baseball squads from 1917 through 1919. He also managed the 1920 Toronto Maple Leafs of the International League to a .701 winning percentage — the best in the team's 83-year history, but only good enough for second place in the league.
In 1921, Duffy was hired as full-time manager of the Red Sox, guiding them for two seasons. Duffy became a scout for the Boston Red Sox in 1924.
Duffy remained on the scouting staff of the Red Sox nearly to the end of his life, retiring in 1953. He died in Boston on October 19, 1954. He had been suffering from heart problems. Duffy's wife Nora died the previous year; they did not have children.