[citation needed] The school takes its name from the Chowanoke tribe of indigenous people who previously inhabited the land on which Murfreesboro and Chowan University stand.

Financial strain from the effects of the Great Depression forced the school to become a two-year institution in 1937.

[citation needed] Two years later, the universities gained autonomy from the Baptist State Convention of North Carolina and established a "good faith and cooperative" relationship with it.

[citation needed] In December 2023, Rosemary M. Thomas was named as its 24th president and the first woman to serve in the role.

[6] Chowan University is accredited by the Southern Association of Colleges and Schools Commission on Colleges to award associate, baccalaureate, and masters degrees, along with other programs accredited by discipline-specific accreditors and approved by state agencies.