The heritage of the News Journal can be traced back to 1889, when a group of Pensacola businessmen founded the Pensacola Daily News. The Daily News printed its first issue on 5 March 1889, with an initial circulation of 2,500 copies. Then, in March 1897, a Pensacolian named M. Loftin founded a newsweekly, the Pensacola Journal. The Journal converted to a daily format a year later.
The two dailies competed fiercely, each driving the other to edge of bankruptcy in the struggle to be recognised as Pensacola's top daily newspaper. By 1922, the Journal was in dire financial trouble, and was eventually purchased by New York businessman John Holliday Perry, who at about the same time also acquired papers in Jacksonville and Panama City. Two years later, Perry bought the Daily News and merged the two newspapers' operations. For the next six decades, the Pensacola Journal continued to appear mornings and the Pensacola News evenings, with a combined Sunday edition as the Pensacola News Journal.
John H. Perry developed the News Journal into an extremely popular and successful newspaper. By the early 1950s, the News Journal had developed into one of the most modern and efficient newspaper operations in the Southeast. Under the leadership of Perry's son, John Holliday Perry, Jr., who succeeded his father in 1952, the News Journal continued to expand. Perry Publications, Inc., eventually owned 28 newspapers throughout Florida.
On July 1, 1969, Perry Publications chairman and president John H. Perry, Jr. announced that the company had sold the two papers to Gannett Co., Inc., then based in Rochester, N.Y., for $15.5 million.
Like many U.S. evening newspapers in the post-war period, the News sustained declining circulation and was folded into the Journal in 1985.
The paper gained nationwide notoriety in 1997 and 1998 with a series of investigative reports about the Brownsville Revival at the Brownsville Assembly of God. The paper had initially written glowing reports about the revival, but after former members told the paper that all was not as it appeared, the News Journal began a four-month investigation that revealed the revival had been "well planned and orchestrated" from the very start. It also called many of the claims made by the church's leaders into question, and delved heavily into the church's finances.
After over a century, the production departments moved to Mobile, Ala., on 2 June 2009.
In August 2014, the Pensacola News Journal moved to its new headquarters at 2 N. Palafox St. The longtime headquarters at 101 E. Romana St. was demolished in 2015 by its new owners, Quint Studer's Daily Convo, who will build apartments, retail shops and a new YMCA on the site.