Guerrero began his career with Motagua in Honduras, playing with the team from 1996 until transferring overseas in 2000. He moved to the English Premiership to play for Coventry City along with compatriot Jairo Martínez. He came back to Motagua in 2002 and then moved to Peñarol in Uruguay in 2004, before his move to the Chicago Fire. He served as Chicago's lone representative in the 2005 MLS All-Star Game; and won the Fire's 2005 Fire/Honda MVP and Fire Defender of the Year awards.
Guerrero has been an important player on the Honduran national team, playing during the 2006 World Cup Qualifiers. He was a member of the national squad who competed at the 2000 Summer Olympics in Sydney.
Guerrero is a permanent resident of the United States.
On November 21, 2007 he was selected by the San Jose Earthquakes in the 2007 MLS Expansion Draft. He was later traded to D.C. United on July 31, 2008 in exchange for a partial allocation. He made his D.C. United debut on August 2, 2008 as a starting left midfielder in a 2-0 win against Kansas City Wizards.