Paxon High School was originally named Paxon Field Junior-Senior High School when it was built in 1954. It included 7th through 12 grades until 1957, when Paxon Junior High was built across the street. In 1996, Paxon became a college preparatory school and an International Baccalaureate school, and took on its present-day name. In 2008, Paxon School for Advanced Studies was ranked number 8 of the 100 best high schools in the nation by Newsweek magazine; 17th in 2007, 28th in 2006, 7th in 2005 and 3rd in 2003.

The site where the school was built was Paxon Air Field, where Bessie Coleman was killed in a plane accident in 1926. Coleman was the first African American (male or female) to become an airplane pilot, and the first American of any race or gender to hold an international pilot license. Paxon Field was Jacksonville’s first airfield, with the exception of the beaches. The Navy used the (grass) airfield for training during World War II, but eventually declared the site excess in January 1947.