After college, Mullaney was with the FBI before returning to basketball as coach at Norwich University in Vermont. Mullaney became head basketball coach at Providence College in 1955. He coached the Friars until 1969, returning in 1981, remaining until 1985. Mullaney went 319-164 during his 18 seasons, a winning percentage of.660. Mullaney won the 1961 and 1963 National Invitation Tournament championships at Providence. Mullaney also took the Friars to the NIT four other times and into the NCAA tournament three times. His assistant and protégé at Providence, Dave Gavitt, went on to be a successful coach of the Friars, taking them to the 1973 Final Four and eventually help founding of the Big East Conference.
Mullaney left Providence in 1969 to coach the Los Angeles Lakers of the National Basketball Association, succeeding Butch van Breda Kolff who took the Lakers to the NBA Finals that year, losing 4-3 to the Boston Celtics. In the 1969–70 season the Lakers overcame several injury problems and finished 46-36, two games behind the first-place Atlanta Hawks in the Western Division. Wilt Chamberlain was lost to injury early in the season and Elgin Baylor was also lost to injury later; both returned in time for the playoffs. En route to the NBA Finals they defeated the Phoenix Suns in the division semifinals and Atlanta in the division finals. The Lakers lost the NBA Finals 4-3 to the New York Knicks. In the 1970–71 season the Lakers finished 48-34, first in the new Pacific Division. The Lakers defeated the Chicago Bulls in the conference semifinal but lost to the Milwaukee Bucks in the Western Conference Finals.
ABA coaching years
In 1971 Mullaney became the fifth coach of the Kentucky Colonels of the American Basketball Association, succeeding Frank Ramsey in 1971. Mullaney coached the Colonels for two seasons before Babe McCarthy succeeded him for the 1973–74 season. In the 1971–72 season the talent-laden Colonels finished with a remarkable record of 68-16, the best ever record in the history of the ABA, winning the Eastern Division. Incredibly, the Colonels lost the 1972 Eastern Division Semifinals to the 44-40 New York Nets, 4-2. Mullaney coached the East team to a 142-115 win in the ABA All Star game that season. In the 1972–73 season the Colonels finished 56-28, good for 2nd in the Eastern Division. The Colonels beat the Virginia Squires 4-1 in the Eastern Division Semifinals, beat the Carolina Cougars 4-3 in the Eastern Division Finals, and lost the ABA Finals 4-3 to the Indiana Pacers. After the 1972–73 season Mullaney left the Colonels to coach the Utah Stars. Mullaney was replaced in Kentucky by Babe McCarthy. Oddly, McCarthy and Mullaney both were named co-ABA Coach of the Year for the 1974–75 season. During the 1973–74 season Mullaney coached the Utah Stars to a 51-33 record, finishing 1st in the Western Division. The Stars defeated the San Diego Conquistadors 4-2 in the 1974 Western Division Semifinals and the Indiana Pacers 4-3 in the 1974 Western Division Finals, losing the 1974 ABA Finals to the New York Nets 4-1. Mullaney coached the West in the 1974 ABA All-Star Game, losing to the McCarthy-coached East 128-112. Mullaney was replaced as coach of the Stars by Morris "Bucky" Buckwalter after that season in Utah. During the 1974–75 season Mullaney coached the Memphis Sounds, finishing with a record of 27-57 and 4th place in the Eastern Division. Their season was ended by Mullaney's old team, the Kentucky Colonels, en route to the Colonels' 1975 ABA Championship. At the start of the 1975–1976 season Mullaney was the coach of the Baltimore Claws but the team folded after a few preseason exhibition games. In December 1975 Mullaney became coach of the Spirits of St. Louis. Mullaney took the helm in St. Louis in midseason after the team opened with a 20-27 record under coach Rod Thorn. Mullaney was the final coach of the Spirits of St. Louis, as at the end of the 1975–1976 season the Spirits, along with the Kentucky Colonels, were the only two ABA teams that did not join the NBA in the ABA–NBA merger.
Post ABA career
After the 1975–76 season Mullaney coached the Buffalo Braves of the NBA. Mullaney was brought on board by the Braves' new owner, John Y. Brown Jr., who had previously had an ownership interest in Mullaney's old team, the Kentucky Colonels. Despite Adrian Dantley earning Rookie of the Yearthe Braves finished in 4th with a 30-52 record. Mullaney coached in Italy and then for Brown University from 1978 through 1981.
