Huber was drafted by the San Diego Padres in the 5th round (139th overall) of the 2000 Major League Baseball draft. He began his professional career in 2000 with the rookie-level AZL Padres. Huber went 1–4 with a 6.60 ERA, and 39 strikeouts in 14 games; 10 starts.
Huber's professional baseball journey began in 2000 with the rookie-level AZL Padres after being drafted by the San Diego Padres in the 5th round of the 2000 MLB draft. His initial season saw him go 1-4 with a 6.60 ERA and 39 strikeouts in 14 games (10 starts).