George Stallings, the manager of the Philadelphia Phillies of the National League (NL), noticed Flick while he played for Dayton. Stallings signed Flick to the Phillies to serve as a reserve outfielder for the team in the 1898 season. Starting outfielder Sam Thompson injured his back after six games, forcing Stallings to play Flick. In his debut game, Flick went 2-for-3 with two singles against Fred Klobedanz. Thompson returned to the team briefly, but reinjured his back and announced his retirement in May, allowing Flick to play regularly. Flick proved himself a capable big leaguer, batting .302 with eight home runs, 13 triples and 81 runs batted in (RBIs). In the 1899 season, he batted .342, with 98 runs scored and 98 RBIs. However, he suffered a serious knee injury in August, and reinjured the knee when he returned to the game too quickly.