Houghton University has long embraced athletics and competitive sports as part of the educational experience of the young people whose lives are shaped by their time here. For many years, students enjoyed "Purple and Gold" intramural competition; even today, older alumni will wear "their color" at chapter meetings and Homecoming.

In 1967, the university developed its first intercollegiate teams and quickly established a reputation for excellent play. Coach Doug Burke led the early men's soccer team, retiring in 1993 with a spot in the National Association of Intercollegiate Athletics' (NAIA) Soccer Hall of Fame. The Highlanders, nicknamed for the rolling hills in the Houghton area, added sports through the years and now support 16 varsity teams in baseball, basketball (M&W), cross country (M&W), field hockey, soccer (M&W), softball, tennis (M&W), indoor and outdoor track and field (M&W) and volleyball.

The Highlanders have earned a reputation for achievements both in the arena of play—with more than 40 appearances in NAIA national tournaments—and in the classroom. In 2006-07, the NAIA began designating "Scholar Teams," whose athletes achieved a combined grade point average of 3.0 (out of 4) or better. The majority of Houghton teams has historically made the list each year.

The athletics programs began a new chapter in their history in 2010, by applying for NCAA Division III membership. After an exploratory year in 2011-2012, the department became a provisional member in 2012 and full-time NCAA members in 2016. The teams currently compete in the Empire 8 Conference.

The teams use their commitment to excellence, both athletically and scholarly, as a platform for their strong and unique emphasis on sports ministry. Houghton coaches and student-athletes are working together to change the culture of sport and to change our culture through sport. Their goal is to make a positive impact on those they play with, those they play against, and those they play in front of.

Founded in 1994, "to help preserve, strengthen and add distinction to the athletic program at Houghton University," the Highlanders Hall of Honor recognizes individuals who have made outstanding contributions to the program, through participation, support or interest. Induction into the Hall takes into account the lives of those honored, acknowledging evidence of discipline, sacrifice, steadfastness, cooperation, commitment and Christian witness. The Hall honors the men and women who have demonstrated—both throughout their career and beyond—the worth of athletics by their mature leadership and their impact on society. A plaque commemorating each member hangs in the foyer of the Nielsen Center.

Today the athletic department operates under a mission that states:

"It is the mission of the Houghton University Athletics Department to glorify God by educating and developing men and women leaders who compete with excellence, lead by character, and exemplify Jesus Christ in our world."