Not all sources completely agree on exact dates, but the Morning Sun traces its origin to the Pittsburg Headlight, a weekly which began publication in 1885, under the ownership of brothers Millard Fillmore (M.F.) Sears and W.F. Sears, and cousin Harry Sears. Within the year, M.F. Sears became the sole owner and took on Clarence W. (C.W.) Moore as his partner. In 1886, the Headlight bought out the Pittsburg Democrat, which had been published by Thomas P. Montfort. Montfort had acquired that publication around 1881, when it was called The People's Exponent (founded 1880), and had renamed it. By 1887, Sears and Moore began publishing the Pittsburg Daily Headlight as a daily paper.
Soon C.W. Moore bought out M.F. Sears' interest, and began publishing with his father, William Moore (d. 1897), as "William Moore and Son", by 1888. Two other sons of William, J.T. and George A. Moore, joined by 1896, and eventually succeeded to the ownership of the paper.
In 1915, Paul Jones founded the Pittsburg Sun, a morning paper. The Moore brothers purchased the publication in 1927, and both the Headlight and Sun were purchased that year by Oscar Stauffer. Stauffer's media holdings developed into Stauffer Communications.
Perhaps the most notable editor of the papers was Frederick W. (F.W.) Brinkeroff (b. Feb. 13, 1885, d. Aug. 13, 1966), who became editor of the Headlight in 1911, and also editor of the Sun in 1927. He served as editor of both papers until his death in August 1966, and was soon after inducted into the Kansas Newspaper Hall of Fame.
In 1966, the afternoon Headlight and morning Sun were merged into the Headlight-Sun. The Morning Sun name was adopted in 1973.
In 1994, Morris Communications announced plans to acquire Stauffer Communications, which by that time was operating 20 daily newspapers (including the Morning Sun) and eight weeklies, in addition to a number of television and radio stations. At the time the circulation was 10,312. In 2007, GateHouse Media media acquired the paper from Morris Publishing Group as part of a larger sale of papers.
As of 2009, the reported circulation of the paper was 9,850.