Two hundred years ago, much of the area of the current Boynton Beach was swampland and there were several lakes in the area. Native Americans living in the nearby areas include the Jeaga, the Ais, and the Tequestas.
Florida was rapidly settled through the late 1800s. Lantana was homesteaded in 1885-1887, West Palm Beach incorporated in 1894, and the East Coast Canal (later renamed the Intracoastal) was extended from Jacksonville to Miami in 1894.
By the end of 1895, the Florida East Coast Railroad had established a train station here and several stores had been opened. Within a few more years, a post office was established, a school and churches were built, and Boynton was making a name for itself for growing and shipping tomatoes (and later pineapples) to the north by train or steamer. A large hotel, The Boynton, was opened on the ocean at the end of Ocean Avenue by Nathan Boynton by 1899. By 1910, the Federal U.S. Census records the population as 670 residents.
The town was incorporated in 1920 as "Town of Boynton," but changed its name in 1941 to "City of Boynton Beach."