In his first five years at Boston College, Mike Holovak compiled a mark of 24–16–5, winning Coach of the Year honors in 1954 from New England football writers. Those efforts were good enough to earn him a new four-year contract on November 22, 1955, but even after four more winning seasons, he was fired on December 3, 1959.

Two weeks after his dismissal, Holovak signed as a scout with the fledgling Boston Patriots, then was named an assistant under Lou Saban on March 29, 1960. After a 5–9 record that year and a 2-3 start in 1961, Saban was fired on October 10 and replaced by Holovak. His first game as Patriots coach was a 31-31 tie (the first in Patriots history) with the Houston Oilers. Finishing with a 9–4–1 record, Holovak matched that record the following year, earning him a new three-year contract, with an option for another year.

In 1963, the Patriots reached the postseason for the first time, despite only compiling a 7–6–1 record. They then defeated the Buffalo Bills in an Eastern Conference playoff, but were then pounded in the AFL Championship game, 51–10, by the San Diego Chargers. The next year, Holovak added the duties of general manager to his job description, and after the team improved to 10–3–1, he was named AFL Coach of the Year on December 15, 1964 and received a new five-year contract.

However, the veteran unit slipped to 4–8–2 in 1965, but rebounded into contention the next season with the addition of rookie running back Jim Nance. Needing only a victory in their final game against the New York Jets on December 17 to reach the AFL title contest, the Patriots instead saw their 1966 season end with an 38-28 upset loss. The defeat was softened somewhat when Holovak again won the league's Coach of the Year accolade.  Age finally caught up with the team over the next two years with the Patriots managing only a 7–20–1 record. The end result was that Holovak was fired from both positions on January 7, 1969, ending his Patriots tenure with a mark of 53–47–9.