Since 1972, home games are played at the 6,300-seat Beeghly Center on the YSU campus.

The team was founded in 1927 and played their first game on December 14, 1927, a 53–24 loss to Thiel College.

Upon reinstatement in 1946, the Penguins joined the National Association of Intercollegiate Athletics (NAIA), where they competed from 1946 to 1960.

YSU moved to Division I in 1981 and joined the Ohio Valley Conference, playing in the OVC until 1988.

The 2022–23 season saw the program win their first-ever conference championship by winning the Horizon League regular-season title, along with their first appearance in the National Invitation Tournament (NIT).

The Penguins have appeared in the NCAA Division II Tournament nine times.