The original Waldo train station was built by the Seaboard Air Line Railway as a two-story structure with a large freight room, and was a divisional headquarters.

In 1930, the top floor and part of the freight room were removed, and in 1963, the old building was replaced by the current structure.

[1] In 1971, most passenger service in the United States was transferred to Amtrak, and the Silver Meteor retained its stop in Waldo.

[3][4] Two years later, the Palmetto was truncated to Savannah, Georgia on November 1, 2004, prompting Amtrak to revive Silver Star service to Tampa along the CSX A-Line shared by the current Silver Meteor, and part of the suspended Sunset Limited, and finally ending passenger service to Waldo.

Today, the station only serves as a stop for Amtrak Thruway bus service between Jacksonville and Lakeland.