No people were injured in the accident near the Florence Castello station.
The railway route between Florence and Bologna, an important north-south connection, was disrupted for many hours, both for regional and long-distance traffic.
Hundreds of passengers were stranded at many stations, including in Rome and Milan.
The railway company Trenitalia reported a total of 36 cancelled high-speed trains, with many other long-distance trains diverted.
It was not clear why a wagon of the goods train derailed, a railway official said, according to the ANSA news agency.
