Irwin coached at the University of Pennsylvania between 1893 and 1895, and managed the Philadelphia major league club during those last two seasons.  In 1894, he angered Penn supporters when a talented first baseman named Goeckle nearly signed with Irwin's major league team just prior to a series of collegiate championship games. Nonetheless, by 1895, Irwin's coaching role at Penn included the selection of players and other duties that traditionally fell to the team captain. Irwin left Philadelphia in 1896 to manage the New York Giants. Relieved of his duties after one season in New York, he was subsequently recruited to manage in Milwaukee. However, he returned to coach the minor league team in his native Toronto instead.  Irwin coached Toronto during 1897 and 1898. He faced arrest on a libel charge in 1898, which stemmed from comments made by Irwin about the actions of the Philadelphia ownership during his time there. Though Irwin turned himself in, it appears that he was never arrested. In 1898, Irwin traded some of his best players to the Washington major league team. The moves were seen as particularly suspect when Irwin was named the Washington manager shortly thereafter. After 1899, Irwin did not return to the major leagues as a coach. He returned for a subsequent term as Penn's coach in 1900, but he left in 1902. In August 1902, Irwin was signed as an NL umpire for the remainder of that season. Irwin, who had previously only filled in for one three-day umpiring stretch in 1881, umpired his first NL game on August 7, 1902. His last umpiring appearance came with the end of the 1902 season on October 3. In fifty games as an umpire, Irwin ejected nine players, including future Hall of Fame inductees Roger Bresnahan and Fred Clarke. Irwin, who had retained partial ownership of the Toronto club, then returned to manage that team for a couple of seasons.  By 1906, Irwin was manager of the Altoona Mountaineers in the Tri-State League. In July 1907, Irwin resigned as manager of the Mountaineers after fans became disgruntled. Even after entering baseball scouting, Irwin briefly managed the 1908 Washington club in the short-lived Union Professional League. The league was plagued by financial problems--including the inability to pay players at times--and it folded less than two months after play began. He was rehired to the Penn coaching staff in 1908.

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