Also in 1997, IU Indy joined the Mid-Continent Conference (now known as the Summit League), and officially changed their nickname to the Jaguars.

Administration of the athletic program fell to the new Indiana University Indianapolis.

[3][4] The official athletics website uses IU Indy as the main brand name, with the Jaguars nickname remaining in place.

The 1989–90 Jaguars defeated Siena Heights in the NAIA Tournament, but lost their next game to Pfeiffer.

The 1990–1991 team advanced to the semifinals of the NAIA National Tournament before losing to Southwestern Oklahoma State.

They were coached by P. Nicholas Kellum who is now a member of the IUPUI Athletic Hall of Fame and was the school's first athletic director and served as the dean of the School of Physical Education for many years.

From 2014 to 2023 the men's basketball team played at the Indiana Farmers Coliseum and returned to The Jungle in 2024.

The swimming team competes at the Indiana University Natatorium, which has a capacity of 4,700.