On November 5, 1894, 78 people met at the "Calaboose" (the city's first jail and police station) and passed the motion to incorporate as a city (two years before Miami), making West Palm Beach the first incorporated municipality in South Florida.

The area that was to become West Palm Beach was settled in the late 1870s and 1880s by a few farmers who staked claims around Lake Worth, a freshwater lake named after Colonel William Jenkins Worth who had fought in the Second Seminole War in 1842. These settlers, which included families such as the Potters and the Lainharts, called the vicinity "Lake Worth Country."

West Palm Beach was the brainchild of Henry M. Flagler, who founded the city as a commercial and residential center to support his 1,100-room Royal Poinciana Hotel on the neighboring island of Palm Beach. The city grew steadily and quickly became the leading metropolitan and governmental center for Palm Beach County.

The city has a total area of 58.2 square miles (151 km²), of which 55.1 square miles (143 km²) is land and 3.1 square miles (8.0 km²) (5.26%) is water.

Orchids, one of the oldest families of flowering plants, can be found all over the world--but they grow especially well in the tropical rainforest climate of "Orchid City".

Palm Beach State College was founded in 1933 as Palm Beach Junior College and was the first public junior college in the state of Florida. On May 30, 1991, the Old Palm Beach Junior College Building was added to the U.S. National Register of Historic Places.

The city only recovered with the onset of World War II, after the construction of Palm Beach Air Force Base (then called Morrison Field) brought thousands of military personnel to the city. Following the attack on Pearl Harbor, Morrison Field was used for training and later as a staging base for the Allied invasion of France, with numerous aircraft departing Morrison to take part in the D-Day invasion of Normandy.

German U-Boats sank dozens of merchant ships and oil tankers just off the coast of West Palm Beach. Nearby Palm Beach was under blackout conditions to minimize night visibility to German U-boats.

Hidden on Peanut Island is an underground fallout shelter built in December 1961 as a safe haven for President John F. Kennedy, whose family's Palm Beach compound was minutes away across the water. The bunker was closed in 1963 following Kennedy's assassination, and its existence was declassified in 1974. From 1998 to 2017, it was open to the public as an historic site.

West Palm Beach became one of the nation's fastest-growing metropolitan areas during the 1950s when the advent of air conditioning made year-round living in a tropical climate more acceptable to northerners. During this period, the city's borders spread west of Military Trail and south to Lake Clarke Shores.