[2] The school opened in the residence of Colonel Jones S. Hamilton, a Confederate veteran who became a millionaire after the war through investments in railroads run by convicts he leased.

In 1921, Guy T. Gillespie of Lexington, Mississippi, began a 33-year presidency during which Belhaven was first accredited, an endowment fund begun, and scholarships made available.

A major fire devastated the college on August 9, 1927, when lightning struck the school's only building.

In 1954, the board of trustees voted to allow the enrollment of male students, making Belhaven a fully co-educational institution.

McFerran Crowe succeeded Gillespie as president and over the next six years he expanded and upgraded the faculty, while also reorganizing and modernizing business operations.

From 1960 to 1961, Robert F. Cooper served as acting president until the board selected Howard J. Cleland, then principal of nearby Murrah High School, to replace him.

Under Cleland's 17-year tenure, an ambitious expansion program resulted in six major new buildings, while enrollment and the college budget tripled.

In his eight years as president he reaffirmed the commitment to Christian service and the covenant relationship with the Presbyterian Church, and installed a more efficient administrative structure.

[2] Verne R. Kennedy followed as president, and was the first Belhaven alumnus to serve as the school's chief officer.

In January 1996, Doctor Roger Parrott became the tenth president of the college, with about 1,300 enrolled students.

[16] They were also a member of the National Christian College Athletic Association (NCCAA), primarily competing as an independent in the Mid-East Region of the Division I level.

The Blazers have been in the World Series 7 of the past 10 years with NCCAA #2 finishes at the national tournament in 2016 and 2018.

The men's soccer team won the 2012 NAIA National Championship, compiling a record of 19–4–1.

Charlie Rugg led the men's tennis team to the 1983 NAIA National Championship.