Rubley was selected by the Los Angeles Rams in the ninth round (228th pick overall) of the 1992 NFL Draft. He spent his rookie season as the team's inactive third quarterback.
Rubley saw action in two NFL seasons in 1993 and 1995. He started seven games for the Rams during the 1993 season. With limited playing time and being waived numerous times by NFL teams, Rubley found success with the Rhein Fire of the WLAF and played briefly with Hamilton Tiger-Cats and Winnipeg Blue Bombers of the CFL.
His most infamous NFL moment, leading to the end of his career, came as a Green Bay Packer in a 1995 game against the Minnesota Vikings. Both starting quarterback Brett Favre and back-up quarterback Ty Detmer got injured in the game, but the Packers and Vikings were tied 24–24 with less than a minute to go and the Packers with the ball on the Minnesota 38-yard line.
On 3rd-and-1, coach Mike Holmgren called for a quarterback sneak. However, Rubley, the only remaining quarterback for the Packers, audibled and called a roll-out. He passed the ball and it was quickly intercepted, giving Minnesota the ball and eventually, the win.
After the game, an incredulous Holmgren commented, "I called a quarterback sneak. He [Rubley] changed the play. He thought he had the choice." Packers General Manager Ron Wolf was equally livid, commenting, "I can't believe this. I think we've exhausted ways to lose here." Rubley himself said, "It was not a real good decision." Rubley was cut later that week, and never appeared in another NFL game, although he was on the Denver Broncos roster the following season.
Rubley served as a consultant for the film The Replacements, specifically coaching Keanu Reeves in his role as the starting quarterback for the fictional Washington Sentinels. Reeves' character, Shane Falco, is loosely based on Rubley.