Allen began his coaching career at the University of Dayton as a graduate assistant, where he earned a master's degree in 1979.

After a six-year stint for the Terriers, Allen finished his coaching career back at Holy Cross, where he led the Crusaders for eight seasons before being fired following a 1–11 campaign.

What happened instead turned out to be one of the single biggest turnarounds in NCAA Division I-AA football history.

In the first-round game, the Terriers defeated the Kurt Warner-led Northern Iowa Panthers, 27–21, in double overtime.

Mark is the current head football coach at Algonquin Regional High School in Northborough, MA, and has been there for over 9 years in total, previously as the Defensive Coordinator.