Miller played high school football and baseball at Lakes High School in Lakewood, Washington. He started three seasons at quarterback while also playing the role of kicker and punter. As a senior, he threw for 3,366 yards with 42 touchdowns, while earning the Player of the Year award. He recorded career totals of 9,003 passing yards and 103 touchdowns. Miller also earned various honors, including First Team
All-State, First Team All-Conference three times, and First Team All-American during his senior year. He helped his baseball team end a 15-year playoff drought.
Miller played for the BYU Cougars from 1997 to 1998. He was the first true freshman in the school's history to start at quarterback. He transferred to play for the Montana Grizzlies from 1999 to 2000. Miller was named the 1999 Big Sky Conference Newcomer of the Year. He was also named First Team All-Big Sky as well as First Team All-American in 1999 and 2000. He played 22 games during his collegiate career for the Cougars and Grizzlies, completing 530 of his 812 passes for 7,211 yards and 52 touchdowns.