The team was founded in 1927 and played their first game on December 14, 1927, a 53–24 loss to
Thiel College. Like many other men's athletic programs, after the 1942–43 season, the program was suspended, but returned in 1946 after
World War II. Upon reinstatement in 1946, the Penguins joined the
National Association of Intercollegiate Athletics (NAIA), where they competed from 1946 to 1960. As NAIA members, the Penguins qualified for the NAIA tournament four times and had an overall record of 5–4 in tournament play, advancing as far as the quarterfinals in 1957 and 1958. YSU joined the NCAA in 1960 and competed at the
Division II level from 1960 to 1981, joining the
Mid-Continent Conference in 1978. During their tenure in Division II, the Penguins qualified for the NCAA tournament nine times and had an overall record of 8–11 in tournament play, advancing as far as the regional finals in 1972. YSU moved to Division I in 1981 and joined the
Ohio Valley Conference. They reached the tournament final in 1984 and 1985, losing both times. They played in the OVC until 1988. The Penguins competed as an independent from 1988 to 1992, then rejoined the Mid-Continent Conference, which by then had become a Division I conference. They reached the tournament final in 1998. They joined the Horizon League in 2001. YSU made their first appearance and recorded their first win in a Division I postseason tournament by playing in the
2013 CollegeInsider.com Postseason Tournament where they went 1–1. 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). In 2025, they reached the final of the
Horizon League tournament for the first time ever. ==Postseason results==