Duffy entered the National League with Cap Anson's Chicago White Stockings in after receiving an offer of $2,000 from the club. Anson initially was unimpressed with the 5'7" 150 pound Duffy telling him, "We already have a batboy." He shortly thereafter earned the reputation of an outstanding outfielder and powerful hitter. Duffy ended up replacing Billy Sunday as the teams's regular right fielder. He switched leagues, joining the American Association's Boston Reds in ; he then returned to the NL with the Boston Beaneaters in , where he enjoyed his best seasons. Playing in Boston from 1891 until , Duffy knocked in 100 runs or more 8 times. In Duffy had one of the greatest seasons in baseball history, leading the league with 18 home runs, with 145 RBI and a .438 batting average (see Triple crown). Duffy's .438 average is the Major League single season batting average record. He played with two other Hall of Fame outfielders during his career, Tommy McCarthy (as half of the "Heavenly Twins") and Billy Hamilton. Duffy finished his career in with 106 home runs which was, at the time, one of the highest career totals ever.
During the 1902 and 1903 seasons, Duffy was player manager for the Western League's Milwaukee franchise and the following season was hired on as player-manager for the Phillies. Duffy went on to coach the Harvard varsity and freshman baseball squads from 1917 through 1919. He also managed the 1920 Toronto Maple Leafs to a .701 winning percentage — the best in the team's 83-year history, but still only good enough for second place in the International League. In 1921, Duffy was hired as full-time manager of the Red Sox, guiding them for two seasons. He had previously been Player/Manager for the Milwaukee Brewers in 1901, the Phillies from 1904 to 1906 and the White Sox from 1910 to 1911.
He later became a scout for the Boston Red Sox from to . Duffy's Cliff, a famous 10-foot-incline replaced by the Green Monster at Fenway Park‚ was named after Hugh Duffy. He was inducted into the Baseball Hall of Fame in 1945, and played much of his career with fellow Hall of Famers Jimmy Collins and Kid Nichols.