The meaning of the name Boca Raton has always aroused curiosity. Many people wrongly assume the name is simply Rat's Mouth. The Spanish word boca, or mouth, often describes an inlet, while raton means literally, mouse. The term Boca de Ratones or Boca Ratones, was a navigational referring to a rocky or jagged inlet, but the original location of Boca de Ratones was Biscayne Bay near present day Miami Beach, according to eighteenth century maps. By the beginning of the nineteenth century, the term was mistakenly applied to the current Lake Boca Raton, whose inlet was closed throughout most of the eighteenth and nineteenth centuries. The "s" and later the "e" were dropped from this title by the 1920s, yet the correct pronunciation remains Rah-tone.

The earliest known inhabitants of the Boca Raton area were the Tequesta Indians, who lived in communities near the ocean as long ago as one thousand years until the eighteenth century. The construction of the Florida East Coast Canal (today's Intracoastal) and the Florida East Coast Railway in the 1890s made the region accessible to a group of resourceful pioneers. By the early 1900s Boca Raton was a tiny agricultural community, many of the farmers specializing in pineapple cultivation. Amongst these were a group of Japanese immigrants under the leadership of Joseph Sakai, who formed a community along today's Yamato Road in 1904.

In May of 1925, the Town of Boca Raton was incorporated at the height of the Florida land boom.