In 1934, Pat Hanley, Dick Hanley's brother and assistant coach, made Holmer his lead assistant. While coaching, BU, Holmer also earned a bachelor's degree in education from the Boston University College of Education. As an assistant, Holmer coached future NFL running back Gary Famiglietti and helped develop Solly Nechtem, who had only played one year in high school, and Walter Williams, who had never played high school football, into top college players. In 1942, Hanley was ordered to active duty with the United States Marine Corps and Holmer succeeded him as head coach.[1] Holmer left B.U. in March 1943 to join the United States Navy Reserve. After he completed his indoctrination course at the Navy pre-flight school at the University of North Carolina at Chapel Hill, Holmer remained at the school as an instructor for the Navy's physical training program for aviation.[4] Boston University did not play football in 1943 or 1944, but returned to the field the following year under interim head coach Robert McKelvey.[5] Holmer was discharged from the Navy later that year and resumed his coaching duties on November 5, 1945.[6] He resigned after a 5–2–1 1946 season and became the physical education director at Cushing General Hospital in Framingham, Massachusetts.[7][2]
Three months after leaving Boston University, Holmer returned to football as the head coach at Colby College.[2] He compiled a 9–17–2 record over four seasons. He resigned on December 14, 1950.[8]