Jimmy 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. In April 2002, Howard played for the United States in the 2002 IIHF World U18 Championships in Slovakia. Playing in six tournament games, he led his team to a Gold Medal 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 on a controversial disallowed goal by Maine forward Derek Damon. 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.