As early as 1890, Henry Flagler, owner of the Florida East Coast Railway began purchasing property, mostly marshland just west of Jacksonville. In 1894, Flagler organized the Jacksonville Terminal Company with ownership being split between five railroad companies: Atlantic Coast Line Railroad, Florida East Coast Railway, and Seaboard Air Line Railway each with 25% ownership, Southern Railway and Georgia Southern and Florida Railway each with 12.5% ownership. Its first Union Depot opened on February February 4, 1895, and completed on January 15, 1897. It later became known as Flagler Depot.
Built on the site of the original one, a new Union Station opened in 1919 and at the time, it was the largest railroad station in the South. At its peak, the terminal handled as many as 142 trains and 20,000 passengers a day. Some of the passenger trains handled in Jacksonville were 18 to 22 railcars long. Within the terminal, there was a restaurant, snack bars, newsstands, a barber shop, florist, a drug store, and gift shops. The Jacksonville terminal had 32 tracks. 29 of those tracks were passenger tracks with platforms.
The station was last used on January 3, 1974; Amtrak moved to a new Jacksonville station several miles north. The station was abandoned until 1982, when a public-private partnership was started, led by former CSX chairman Prime F. Osborn III. The building reopened on October 17, 1986 as the Prime F. Osborn III Convention Center.
Even though the station has since been renovated, the tunnels which were built to bring passengers safely under the platforms to board trains on far tracks, have been buried and forgotten. Each platform had its own ramp which connected with the main tunnel which led to the main building. For the most part, the tunnels remain intact and are currently filled with 3-4 feet of water, roaches, rats, and various other critters.