JTA is a unique state agency, established by state statute in 1955, as the first limited access highway ("expressway") development agency in the State outside of the State Road Department (now FDOT). At that time, the mission was to build and expand the expressway system serving Jacksonville, the gateway to Florida's east coast. The first assignment was the completion of Interstate 95 including the Fuller Warren Bridge and completion of the Mathews Bridge. This was followed by further road expansion and a new Hart Bridge over the St. Johns River. In the 53 years since, JTA has looked to the future and planned roads and expansions to prevent traffic congestion. Some of these projects include J. Turner Butler Boulevard, Dames Point Bridge, and most recently, the completion of Wonderwood Connector. Funding for JTA road and bridge projects was from tolls on the projects, including bonds backed by these toll revenues.

In 1971, the City faced a crisis in the privately-owned mass transit company, Jacksonville Coach Company. In response to the City's urgent request for JTA to broaden its transportation mission to include mass transit in addition to roads and bridges for the greater Expressway System, JTA and local Florida state legislators undertook an amendment to JTA's state statute to permit the acquisition of the Jacksonville Coach Company operations by Jax Transit Management, a wholly-owned public benefit corporation of the JTA. This acquisition marked a new chapter in JTA's relationship with the City of Jacksonville, as mass transit operating shortfalls were the subject of partial funding by the City to JTA. JTA had theretofore relied solely upon its toll revenues to fund its road and bridge projects in Duval County.

In 1988, again at the request of the City of Jacksonville, JTA agreed to remove its toll booths in exchange for receiving a voter-approved transportation sales surtax of one-half of one percent on taxable sales in Duval County. This sales surtax revenue has been put to work by JTA to build roads and bridges in Duval County, to fund mass transit, and to plan and design the future transportation facilities which have and will make possible the efficient movement of people and freight in and through Duval County and the surrounding counties. Of note, if the tolls were still in place today, toll revenues would greatly exceed the transportation sales surtax (approx. $120 million versus approx. $70 million per year). The additional revenue would be used by JTA for facilities maintenance, new transportation facilities, transportation maintenance, and future transportation planning and design, including commuter rail, light rail and major beltway (shared right-of-way) projects.