In a career that spanned 31 years, Fernandes served as Columbia's head baseball coach for 23 seasons, while also fulfilling the duties as the Ivy League school's associate athletics director for intercollegiate sports programs.
In 1977, Fernandes joined Columbia University as the associate athletic director and was named head baseball coach in 1978.
Over his coaching career, Fernandes guided the baseball team to 359 victories from 1978-98 and 2003-05. During that time, he coached 24 players who advanced to the professional leagues, including three major leaguers — the Minnesota Twins' Gene Larkin who had the game-winning hit in the 1991 World Series, National League pitcher Frank Seminara and outfielder Fernando Perez of the Tampa Bay Rays.
Fernandes coached 28 All-Ivy League first team players, a trio of Ivy League Pitchers of the Year, and an Ivy League Player of the Year. In 1987, the Lions won a then program record 28 games and led the nation with its 2.12 earned-run average. In 1993, Columbia won the Ivy League Gehrig Division title.
Fernandes was a member of the NCAA Division I Baseball Committee from 1997-2001. He also served as an NCAA representative at its NCAA Division I post-season baseball regional and super regional competitions across the nation.
Concurrent with his position as head baseball coach, Fernandes also served as an associate athletics director for intercollegiate sports programs at Columbia. In this capacity, he was responsible for the day-to-day administration of Columbia's most visible sports programs, including football and men's basketball.
In 2001, the All-America Football Committee named Fernandes as its Outstanding Associate Athletics Director. Within his community, he co-founded and co-directed the Coaches 3 Youth Baseball Camp from 1977-80 and the Paul Fernandes Baseball Camp from 1990-2005. The latter was the first at the university to serve youth in the Bronx, Manhattan and Harlem.
Following his retirement from Columbia University in 2008, he was Director of Championships and Scheduling for the Ivy League Office from 2008-2010. Fernandes is also a member of the C.W Post College Baseball Hall and SUNY Corland Athletics Hall of Fame.
