After he retired as a player, Hoaglin served as an assistant coach for the Detroit Lions (1978–1984), New York Giants (1985–1992), New England Patriots (1993–1996), and Jacksonville Jaguars (1997–2000), serving under the Bill Parcells coaching tree during his stints at the last three franchises.
He was an assistant coach for the Giants during their Super Bowl XXI and Super Bowl XXV championship seasons under Parcells, then won an AFC Championship at New England under Parcells in 1996 before the Patriots fell 35–21 to the Green Bay Packers in Super Bowl XXXI.
Parcells resigned from the Patriots to take the head coaching job with the New York Jets after that loss, but Hoaglin joined fellow Parcells coaching tree disciple Tom Coughlin in Jacksonville as the tight ends coach. During his time there, the Jacksonville Jaguars won two AFC Central Division titles, reached the playoffs in three consecutive seasons, and played in the 1999 AFC Championship Game.