After playing college football for the California Golden Bears, he was selected by the Baltimore Ravens in the first round of the 2003 NFL draft.

He earned the 1998 California State Player of the Year honors after an outstanding senior season at William S. Hart High School in Santa Clarita, CA.

Because of this, he was considered by many to be the best prospect to emerge from The Valley Region of Los Angeles since John Elway came out of Granada Hills High School in 1979.

During the 1998 season, Boller also played the position of safety on defense, and intercepted a pass in the final minute of the sectional championship game.

He was inactive for most of the rest of the season, being replaced by backup Anthony Wright, as he also had to have surgery to repair a muscle in his quadriceps.

The Ravens held their own in the first half, limiting the Colts to only 3 points, and Boller looked solid in the pocket, leading the offense down the field to the red zone several times.

But it did not last, as Boller was injured in the third quarter, suffering a bad case of "turf toe", that would wind up keeping him out of action for 7 games.

In Week 6 of the 2006 NFL season, McNair was sacked by Carolina Panthers defenders Mike Rucker and Chris Draft.

Faced with a 9-point deficit with 5:10 remaining, Boller connected with Mark Clayton for a 62-yard touchdown pass to start a comeback attempt.

Then, after McNair's throwing hand was stepped on against Cleveland on Dec 17, Boller led the Ravens to victory with a 13-of-21, 238-yard and two-touchdown performance (112.3 passer rating), one touchdown being the game highlight, when he connected with explosive rookie receiver Demetrius Williams for the 77 yard score.

With McNair as the starting quarterback the Ravens improved to a franchise best mark of 13–3 on the season, as compared to only going 6–10 the previous year with Boller at the helm.

After Week 10, which featured a humiliating loss against the Cincinnati Bengals, during which McNair committed 3 fumbles, it was decided that Boller would officially be the starting quarterback for the remainder of the season.

Backup rookie quarterback Troy Smith played the remainder of the game, leading the team into overtime, where they eventually lost, 22–16, giving the Dolphins their sole win of the season.

The 2007 Ravens ended their season with a record of 5–11, which led to the firing of head coach Brian Billick and the drafting of future quarterback Joe Flacco.

Boller was given the starting job against the New England Patriots in the 2008 pre-season opener, but following another injury suffered in a preseason game against the Minnesota Vikings, his season ended when the Ravens placed him on injured reserve on September 3.

[8] An unrestricted free agent in the 2009 offseason, Boller signed with the St. Louis Rams on April 4 as the backup to starting quarterback Marc Bulger.

[12] In October, Boller became the Raiders' starting quarterback after Jason Campbell suffered a collarbone injury against the Cleveland Browns.

An unrestricted free agent in the 2012 offseason, Boller signed with the San Diego Chargers on July 27, 2012, after backup Charlie Whitehurst suffered a knee injury in training camp.