The special primary election was held on April 11, 2006. A candidate who received a majority of the vote would have served out the rest of Cunningham's term. As no candidate won a simple majority, the top vote-getters in each party, DemocratFrancine Busby and Republican Brian Bilbray, competed in a runoff special general election held on June 6, 2006, the same day that primaries were held for the November 2006 general election.
Bilbray won the special election 49 percent to 45 percent and was sworn in as a U.S. Representative on June 13, 2006. In the June 6 primary election for the November 2006 election, both candidates won their party's nomination. In the November 2006 general election rematch, Bilbray won re-election.