Brunell played college football for the Washington Huskies and was selected by the Green Bay Packers in the fifth round of the 1993 NFL draft.

Within their second season, he helped the team obtain the franchise's first winning record, playoff berth, postseason victories, and AFC Championship Game appearance.

Brunell went on to guide Jacksonville to four consecutive playoff runs within their first five seasons, the first NFL expansion team to do so, and clinched the franchise's first division title in 1999 en route to a second AFC Championship appearance.

Following his 2004 departure from Jacksonville, Brunell played for the Washington Redskins, New Orleans Saints, and New York Jets until retiring in 2011.

Brunell was the starting quarterback for the St. Joseph High School Knights of Santa Maria, California, in the 1985, 1986, and 1987 seasons.

Irrespective of their final ranking, the Huskies, with Brunell's star rising, seemed set to soar to even loftier heights in 1991.

Brunell would be given an opportunity to lead series on a part-time basis in the remainder of Husky games as the season progressed, typically at least one drive in each 2nd quarter in addition to the second half.

The 1991 Washington team defeated every regular-season opponent with most games providing plenty of playing time for younger and backup players.

On January 1, 1992, Brunell played a small role (throwing a touchdown pass to Mario Bailey) in Washington's second straight Rose Bowl victory, this time over Michigan.

However, during the week of November 2, 1992, the Los Angeles Times ran an exposé on Washington football wherein current starter Hobert was implicated in actions seemingly in violation of NCAA rules.

On October 20, 1994, Brunell made his professional regular season debut during a 13–10 overtime loss at the Minnesota Vikings in Week 8.

Brunell became a restricted free agent after the 1994 NFL season and received a contract offer from the Philadelphia Eagles, who had just hired former Green Bay Packers’ defensive coordinator Ray Rhodes as their new head coach.

[8] Rhodes hired former Green Bay Packers’ wide receivers coach Jon Gruden to be the Philadelphia Eagles’ offensive coordinator and worked out a trade to acquire Brunell.

Brunell was reluctant to accept the five-year contract offer from the Philadelphia Eagles as he did not want to spend his twenties as a backup quarterback behind Randall Cunningham.

With Brunell starting, the Jaguars won an AFC Central Division title and became the first NFL expansion team to make the playoffs three times in its first four seasons of play.

During the 2004 season, limited by a hamstring injury, Brunell struggled and would be benched midseason for backup quarterback Patrick Ramsey.

Brunell's most prolific moment in the 2005 season was during Week 2, when he completed two long passes to wide receiver Santana Moss for two touchdowns in the final four minutes of the fourth quarter to defeat the Dallas Cowboys on Monday Night Football, 14–13.

[12] On November 13, 2006, after winning only three of their first nine games of 2006, Brunell was benched in favor of Jason Campbell, Washington's 2005 first round draft pick.

On February 7, 2010, for the Super Bowl, Brunell served as the backup QB behind Drew Brees, and the holder for Garrett Hartley.

[17] In April 2012, Brunell stated that he would like to play another season if the opportunity presented itself, contradicting a report from the Florida Times-Union that he was ready to retire.