At the end of the 1994 season, the Cubs hired MacPhail as their president and chief executive officer.[4] MacPhail demoted Larry Himes, the Cubs' general manager,[1] and hired Ed Lynch to fill the role.[5] The Cubs reached the playoffs when they won the National Leaguewild card spot in 1998. They won the National League Central division in 2003.[6] MacPhail served with the Cubs until the end of the 2006 season, when he stepped down and was succeeded by John McDonough.[7]
Peter Angelos, the owner of the Baltimore Orioles, hired MacPhail as the team's president of baseball operations on June 20, 2007.[3] Before the 2008 season, MacPhail traded Érik Bédard for a package that included Adam Jones and Chris Tillman. He acquired J. J. Hardy after the 2010 season and Chris Davis and Tommy Hunter at the trade deadline in 2011. He also hired Buck Showalter as manager during the 2010 season.[6] MacPhail's contract expired at the end of the 2011 season, following the Orioles' 14th consecutive losing season, and he opted to leave the team.[8] Many of the players acquired by MacPhail, as well as Showalter, helped the Orioles reach the postseason after MacPhail's departure.[6]
On June 29, 2015, the Philadelphia Phillies hired MacPhail as a special assistant to Pat Gillick, the team's president. MacPhail succeeded Gillick as president at the end of the 2015 season.[9] On December 11, 2020, he was succeeded by David Dombrowski.[10]