Howell attended Jesuit High School in Sacramento, California where he was a four-year varsity letterwinner. In his senior season, he was 10–0 with a 0.09 ERA and 137 strikeouts, earning California Player of the Year, Sacramento Player of the Year and all-city honors in 2001, as well as being named a first-team All-American by USA Today. He set a section play off record with 47 strikeouts in 22 innings in 2000 as a junior and played in various international tournaments, including winning silver medals at the 2001 Junior Pan American Games, the 2000 International Baseball Association Foundation Games and the 1998 and 1999 AAU National Championships.\n', '

Howell was drafted by the Atlanta Braves in the 2nd round of the 2001 MLB draft but chose to accept a scholarship to the University of Southern California, where coach Mike Gillespie said of him, "J.P. is a phenomenal freshman talent." He was 3–4 with a 6.32 ERA as a freshman for the Trojans. He left the program and, after briefly considering transferring to Cal State Fullerton, instead chose to transfer to the University of Texas.\n', '

Howell was 10–2 with a 2.52 ERA as a sophomore for the Longhorns and 15–2 with a 2.13 ERA as a junior. He led the Longhorns to an appearance in the 2004 College World Series championship series. Howell had the lowest ERA in the CWS that year at 0.77. He was selected as 1st team College All-American and Big 12 Conference Pitcher of the Year.\n', '

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