In 1989, Jerry Jones, the new owner of the NFL's Dallas Cowboys and long-time friend of Johnson's, asked him to be the new head coach, replacing Tom Landry. He eventually led the Cowboys to consecutive Super Bowl victories in 1992 and 1993, before quitting after the season following a feud with Jones.
After briefly being a TV analyst, he joined the Miami Dolphins in 1996, replacing then–head coach Don Shula. He remained with the team until retiring in 1999. He then became a TV analyst again for Fox Sports, and (as of 2003) he is part of their pregame show.