Howard began his junior career playing for the Westport Rideaus of the Eastern Ontario Junior Hockey League, where he played from ages 14–16 before joining the U.S. National Team Development Program. He played with the U.S. National Under-17 and U.S. National Under-18 teams during the 2001–02 season, playing 9 games with the Under-17 team and 26 games with the Under-18 team for a total record of 22–11–1 with four shutouts and was subsequently named USA Goaltender of the year. Howard then attended the University of Maine and played for their men's ice hockey team, the Maine Black Bears, for three seasons. While at UMaine, Howard led the Black Bears to the 2003–2004 Frozen Four championship game, losing 1–0 to the University of Denver. While Howard was playing for the Black Bears, he was drafted in the 2nd round of the 2003 NHL Entry Draft by the Detroit Red Wings. During his three seasons with the Black Bears, Howard set team and league records.
Beginning with the 2005–06 season, Howard began his career in the AHL with the Grand Rapids Griffins where he was occasionally called up to play for the Detroit Red Wings of the National Hockey League. He became the only NHL goalie to face a penalty shot in each of his first two games. Howard's inaugural season in the AHL became what is still one of his best in professional ice hockey. During this season he set many personal records as well as franchise records, including being the first Griffin named to the AHL's All-Rookie Team and helping establish the Griffins franchise win streak record of 12.