Howard started his pro career straight our of high school, playing with the North Jersey Imperials of the USISL. He was signed by Major League Soccer in 1998 and was assigned to the MetroStars, for whom he played until 2003, the last three seasons as the starting goalkeeper. He was named MLS's Goalkeeper of the Year in 2001 and to the league's Best XI in 2001 and 2002, the year he was first capped for the United States National Team. Manchester United signed Howard in the middle of the 2003 MLS season, and he immediately assumed a starting role for the English club.
Howard suffers from a mild form of Tourette's Syndrome and was named MLS's Humanitarian of the Year in 2001 for his work with children infected with Tourette's.