Chartered on January 20, 1887, Nebraska Wesleyan University had an initial enrollment of 96. The initial teaching and administrative staff at this time totaled eight, including the chancellor.
In September 1887, the cornerstone was laid for Old Main, the defining building of the campus. Still with no stairways, windows, or flooring on some floors, classes began in September 1888. The first graduating class was four women in 1890. The second graduating class, in 1891, was made up of four men. Nebraska Wesleyan received accreditation by the North Central Association of Colleges and Secondary Schools in 1914.
The school is located in the former town of University Place, Nebraska. Today, it is part of Lincoln, Nebraska; the surrounding neighborhood is a historic residential and shopping area of Lincoln.
Early on, Nebraska Wesleyan was a college of liberal arts; schools of art, business and education; a music conservatory; an academy (high school) also comprising an elementary school and kindergarten. The high school was discontinued in 1931, and the primary schools in 1941 (grade school) and 1942 (kindergarten). Nebraska Wesleyan offered a Master of Arts degree until 1937.
Nebraska Wesleyan has been associated with four emblems in its history, featuring the Sunflower (1894-1907), the Coyote (1907-1933), the Plainsman (1933-2000), and the Prairie Wolf (2000-present). The school colors of brown and gold are a tribute to the first emblem.
A fire on November 17, 2006, at the Phi Kappa Tau fraternity house killed 1 brother and sent 3 others to the hospital in critical condition. The Lincoln Police later cited 2 men and arrested 1 other on hazing charges as well as illegal possession of fireworks, although not in connection with this fire, resulting in suspension of the fraternity from campus for two to four years. Phi Kappa Tau has returned to Nebraska Wesleyan University in Fall 2011. 
Nebraska Wesleyan University ranks 8th of all universities (4th within NCAA Division III) for students who have won All America awards. Nebraska Wesleyan University student athletes also rank third in Division III and fifth for all universities for NCAA Postgraduate Awards.