The city was first Incorporated in 1844, however certain areas such as East Milton, Point Baker, and Bagdad remain unincorporated.

Milton is located in the geographic center of Santa Rosa County, and it is bordered by Pace to the west, and Navarre to the south.

Most notable were "Hell-Town" (muggy, inhospitable land covered with briars, mosquitoes, thorns, snakes), "Jernigan's Landing", "Scratch Ankle" (due to the briars that grew along the riverbank), and "Hard Scrabble".

[7] According to Florida historian Allen Morris, "Just which Milton was honored by the final name is a dispute.

"[8] Milton was settled in the early 1800s as a small village centered on the lumber industry.

[9] During the Civil War, much of Milton was burned by Confederate forces retreating from the Union capture of Pensacola on May 2–4, 1862.

After the Southern forces evacuated, the Union troops had a small garrison in nearby Bagdad, where they had a base for expeditions in the surrounding area.

[13] Judges from Escambia County sentenced criminals to be confined to Milton, which was nicknamed "Hell Town" by its residents.

An old story from the area tells of the Rough Riders passing through Milton on their "best behavior".

Construction for a new hospital began that year, and in December 1972, the Santa Rosa Medical Center was opened.

On March 31, 1962, an F3 tornado hit the northwest side of Milton, causing 17 deaths and 100 injuries.

Santa Rosa Medical Center (SRMC) is a 129-bed general hospital in Milton.

SRMC is the primary provider of hospital-based healthcare services and emergency medicine in Santa Rosa County.