Daboll began his NFL coaching career with the New England Patriots as a defensive coaching assistant in 2000 before being promoted to wide receivers coach for the Patriots in 2002. After the 2006 season, he left the Patriots to serve as the Jets' quarterbacks coach.
In 2009, Daboll joined Eric Mangini's staff in Cleveland as offensive coordinator. Under Daboll the Browns had the NFL's 32nd ranked offense in 2009  and the 29th ranked offense in 2010. Daboll was named Offensive Coordinator of the Miami Dolphins under Tony Sparano in 2011, with his Dolphins improving from 30th in the league to 20th in overall offense. On February 6, 2012 the Kansas City Chiefs announced the hiring of Daboll as offensive coordinator, replacing the retired Bill Muir. Daboll had previously worked with Chiefs head coach Romeo Crennel, general manager Scott Pioli and quarterback Matt Cassel in the New England Patriots organization. On January 14, 2013, the New England Patriots announced that he would be brought back in a coaching capacity for the remainder of the Patriots 2012-2013 season.