Schottenheimer was born in Denver, Colorado. He prepped at Blue Valley High School in Stilwell, Kansas, where he quarterbacked his team to the Kansas Class 5A state football championship as a senior in 1991, while earning first-team all-state and honorable mention high school All-American honors. He threw for 2,586 yards and 26 touchdowns in his career.
Schottenheimer first attended the University of Kansas in Lawrence, Kansas, where he was a member of the Kansas Jayhawks football team for a single season in 1992 serving as a back to starting quarterback Chip Hilleary. He transferred to the University of Florida in Gainesville, Florida, sat out a year as required by NCAA transfer rules, and then played for coach Steve Spurrier's Florida Gators football team from 1994 to 1996. Schottenheimer served as backup to starting quarterback Danny Wuerffel, and was a member of the Gators' 1996 Bowl Alliance national championship team. During his college playing career, he completed twenty-five of thirty-eight passes (65.8%) for 290 yards and two touchdowns, and also ran for a touchdown.
Schottenheimer graduated from Florida with a bachelor's degree in exercise and sports science in 1997.
Schottenheimer was an assistant coach from 1997 to 2005 with the St. Louis Rams, Kansas City Chiefs, Syracuse Orange, and USC Trojans, including as quarterback coach for the Washington Redskins and San Diego Chargers. He was an assistant under his father, Marty Schottenheimer, in three of those coaching positions: Kansas City Chiefs, Washington Redskins, and San Diego Chargers.
In 2006, he became offensive coordinator for the New York Jets and, in early 2007, Schottenheimer's name was floated around as being a possible replacement for the departed Nick Saban as the Miami Dolphins head coach. He later removed his name from consideration for the Dolphins head coaching position, preferring to stay with the New York Jets.
After the 2008 NFL season, when Jets coach Eric Mangini was fired, Schottenheimer was one of the first candidates interviewed for the open head coaching position. However, he eventually lost out to Baltimore Ravens defensive coordinator Rex Ryan. On January 13, 2009, Schottenheimer announced that he was staying with the Jets as Offensive Coordinator and would not interview for the head coaching vacancy in Buffalo.
On January 10, 2012, Schottenheimer announced he would not return to the Jets for the 2012 season. On January 21, 2012, Schottenheimer became the offensive coordinator of the St. Louis Rams.
On January 7, 2015, it was announced that Schottenheimer would take over as offensive coordinator and quarterbacks coach for the Georgia Bulldogs football team of the University of Georgia, under head coach Mark Richt. Following Richt's firing at the end of the 2015 season, Schottenheimer announced on December 14 to his position players that he would not return as a Georgia Bulldogs assistant coach in 2016.
On January 18, 2016, the Indianapolis Colts announced that they had hired Schottenheimer as their quarterbacks coach.