The area that is now Jupiter was originally labeled on Spanish maps as Jobe or Jove (pronounced "Hoe-Bay"), named after the local Pre-Columbian Native American village and tribe (which may have been a sub-tribe of the Jaega). By the time the English acquired Florida in 1763, the Jobes had been wiped out. The name was confused with the variant name of the Roman god Jupiter and the new name stuck.
In January 1838, after the Second Battle of the Loxahatchee, Major General Thomas Jesup marched his army east to triangular peninsula between the northwest and southwest forks of the Loxahatchee River. There they built a wooden stockade they named Fort Jupiter. Tennessee Volunteers under Major William Lauderdale that comprised part of Jesup's army camped west of the fort. Lauderdale and his men cut a military trail due south to New River (where they built another wooden stockade) and on to Fort Dallas on the Miami River. Fort Jupiter was abandoned in 1842 at the end of the Second Seminole War. It was later repaired in 1855 and reoccupied for a short time during the Third Seminole War before being abandoned for good without ever being attacked.
In 1855, the Federal government created Fort Jupiter Military Reservation encompassing 9088 acres. The original reservation included not only the site of the fort, but also the location of the planned Jupiter Inlet Lighthouse (completed in 1860) and much of what would later become the town of Jupiter (founded 1880s, incorporated 1925). In 2009, the last remaining 120 acres of the original reservation (including the lighthouse) were designated the Jupiter Inlet Lighthouse Outstanding Natural Area (JILONA).
By 1900, Fort Jupiter itself had completely decayed and the property became part of Pennock Plantation, owned by a Quaker pioneer family who grew ferns and raised dairy cattle until the 1960s. Although the area is now an expensive housing development it still bears the name Pennock Point and one of the roads there is named Old Fort Jupiter Road.
Sources: Loxahatchee River Historical Society and "Guns across the Loxahatchee" by Richard Procyk.