Building on the strong tradition of athletics at Houghton – and the proud heritage of the Purple and Gold – the college launched its intercollegiate athletics program in 1967.

As the first varsity teams took the field that fall, the campus took on a project to find a name for the student body to rally behind. The resulting selection process took longer than expected, spanning three months and involving three separate votes, but Houghton Highlanders came out on top.

The student body also considered Hawks, Lancers, Royals, Golden Eagles, Purple Chargers, Warriors, Indians and Braves. The entries were required to meet the criteria of being significant and symbolic of Houghton, either religiously or historically.

Purple and gold were maintained as the official team colors.

Highlanders fit from a geographic standpoint, due to the campus's hillside location overlooking the Genesee River. Historically, the Highlander name has strong ties to Scotland, and while there is no direct connection to Scotland in Houghton's history, a creative poem penned by Ruth Brooks Luckey brought the story of the fictitious Angus McMillen to life in the minds of the Houghton faithful. The story chronicles the journey of McMillen from the Scottish Highlands to Houghton, N.Y., and the role he played in the formation and early life of the college.

While there was never an official mascot or logo over the first 30 years of intercollegiate athletics, the Houghton Highlander drew on Scottish influences in its visual representation, with students donning kilts and Scottish themed outfits to support the Houghton teams and unofficial logos featuring marching bagpipers and sword-wielding warriors. The bagpipes have also been incorporated into various campus and athletics events.

The Department of Athletics initiated a branding project in 2004 that resulted in the creation of the current Houghton visual identity. The primary Highlander logo features a waving flag above the words "Houghton Highlanders." In the center of the flag is a rampant lion similar to what appears on the Royal Banner of Scotland. The rampant lion is shown as a profile of a lion standing upright, with forelegs raised as if to strike. The lion itself represents authority, strength, power, royalty, justice and courage. From a Biblical perspective, the lion depicts authority and power, with Christ referred to as the Lion of Judah.

While creating a new identity and name for Houghton athletics was considered, the overwhelming response – with input provided by current students, faculty, staff and alumni – was to keep the Highlander name and the purple and gold colors, although the colors were updated. The purple was darkened and the gold became less of a yellow and more of a lighter athletic "gold".

In 2016, Houghton introduced the official lion mascot to campus.