At the beginning of 2005, "Baseball America" listed him as the No. 1 pitching prospect in baseball and No. 2 overall behind Joe Mauer. Hernández continued his success in 2005 with the Triple-A Tacoma Rainiers in the Pacific Coast League, posting a 9–4 record with a league-leading 2.25 ERA and 100 strikeouts in just 88 innings. He was selected for the Triple-A All-Star Game but did not participate as he spent a month on the disabled list with shoulder bursitis. He was also named the PCL Rookie of the Year and PCL Pitcher of the Year.