Following his college career Brunner was selected 16th in the 2008 MLS SuperDraft by New York Red Bulls. He initially signed a senior contract, but when the Red Bulls signed Andrew Boyens, they tried to move him down to the developmental roster. However, Brunner refused to take the pay cut and left the team. He signed with Miami FC of the USL First Division of May 20, 2008. Brunner made his first appearance for Miami on June 14, 2008, when he came on as a substitute and played for five minutes.
He made his Columbus debut against Colorado Rapids on April 11, 2009, and scored his first career professional goal on June 20, 2009, against FC Dallas.
On November 24, 2010, he was selected by the Portland Timbers in the 2011 MLS Expansion Draft.
On December 3, 2012, he was traded to the Houston Dynamo in exchange for allocation money.