The Giants released McGinnity on February 27, 1909, when McGinnity decided to pay for his own release. Later career McGinnity purchased the Newark Indians of the Class-A Eastern League (EL) for $50,000 ($ in current dollar terms) in 1909 from Frank J. Farrell. The press reported that McGinnity would operate the team as a farm team of the Giants, though he denied these reports. When McGinnity could not retain manager Harry Wolverton, he stepped in as player-manager for the Indians. That season, he had a 29–16 record. His 422 innings pitched and 11 shutouts set EL single-season records. He also won both games of doubleheaders on August 27, 1909, and July 23, 1912. McGinnity played for and managed the Indians through 1912. The Indians finished second in the EL in 1909 and 1910. McGinnity sold his interests in the Indians to Ebbets and Ed McKeever and purchased the Tacoma Tigers of the Class-B Northwestern League for $8,500 ($ in current dollar terms), spending another $50,000 ($ in current dollar terms) on the franchise in renovating the stadium. He served as player-manager of the Tigers at the start of the 1913 season, but stepped down as manager, hiring Russ Hall to serve as manager in June. McGinnity sold stock in the team in 1915 in order to afford operating expenses. He also briefly played for the Venice Tigers of the Class-A Pacific Coast League in 1914. McGinnity sold the Tigers and purchased the Butte Miners of the Northwestern League in 1916, serving as player-manager and bringing with him several players from Tacoma. In June 1917, he sold his stock in the team and secured his release. He played for the Great Falls Electrics of the Northwestern League for the remainder of the 1917 season. He later became the manager of the A. E. Staley factory baseball team. McGinnity served as player-manager of the Danville Veterans of the Class-B Illinois–Indiana–Iowa League in the 1922 season and Dubuque Climbers of the Class-D Mississippi Valley League during the 1923 season. With Dubuque, McGinnity won 15 games at age 52. One of those wins was a shutout, pitched in a record one hour and seven minutes. Two years later, he returned to play for Dubuque and the Springfield Senators of the Illinois–Indiana–Iowa League during the 1925 season. He pitched in his final professional game on July 28, 1925, after participating in an old-timers game earlier