1900 to 1945 In 1900, Muhlenberg launched its football program, which was the college's first varsity sport. In 1925,
Haps Benfer became Muhlenberg head football coach, and the team finished the
1925 season 6-3-1. From 1936 to 1945,
Doggie Julian was head coach. He recorded a career record of 56–49–2. Julian was also head basketball coach during this time and, from 1942 to 1944, head baseball coach.
1946 to 1997 In 1946,
Ben Schwartzwalder became head football coach. In
his first season, he guided the Mules to a 9–1 record and a national championship with Muhlenberg defeating
St. Bonaventure University in the
Tobacco Bowl. In 1949, Schwartzwalder departed to coach
Syracuse.
1997 to 2018 Mike Donnelly became the head football coach in 1997. Despite a 1–9 inaugural season, Donnelly turned the team around; from 2000 to 2004, the Mules won five straight
Centennial Conference championships and earned five straight postseason berths. In 2007, the Mules again won the Centennial Conference and received another berth in the NCAA playoffs, winning their first-round game before falling in the second round. Donnelly's team won the Centennial Conference again in 2008 and earned a playoff berth, but lost in the playoff's first round. In 2010, they returned to the playoffs with the same result. Since the 2000 season, Muhlenberg has compiled a 66–28 overall record in the Centennial Conference, second best among all active and former members behind only
Johns Hopkins University. Seven times in the 2000s, the Muhlenberg football team won the Centennial Conference championship.
2018 to present Nate Milne became Muhlenberg's head football coach in the 2018 season. He has a 35–5 record over his first three seasons. In 2019, he was named
AFCA Coach of the Year Award for
NCAA Division III. ==Conference affiliation==