After graduating from Florida, Johnson was not selected in the 2000 NFL Draft, but signed with the Atlanta Falcons as a free agent. As an Atlanta Falcon in 2002, Johnson led the team to a 17–10 victory in a start against the New York Giants. In the game, Johnson completed 19 of 25 passes for 257 yards and one passing and one rushing touchdown. In four seasons with the Falcons, he started eleven games and passed for 2,600 yards. He has since played three additional seasons, mostly as a back-up or practice squad quarterback for three different teams. On September 1, 2007, he was released by the Cincinnati Bengals after playing the preseason as a backup to Carson Palmer.
Johnson was also a second-round draft pick in 1996 for the Tampa Bay Devil Rays, playing as an infielder in their minor league system in 1996 and 1997 before suffering a rotator cuff injury and leaving to concentrate on football full-time.
Football Outsiders uses the term called "the Doug Johnson Effect," referring to "part-time players who had a very good performance the previous season in only one or two games," as a caution against overvaluing NFL players for the next season.