The crash happened near Strasbourg on what was supposed to be the final test run of the new high-speed line from Paris to the northeastern city.
Systra, the company responsible for railway tests, was charged after two days of questioning. SNCF is due before judges on Wednesday.
Systra was drawn into the case over its decision to try a test speed of 330 kilometres – the limit of its capability - rather than 187 kilometre per hour – its operating speed , according to a report submitted to the courts by prosecutors in October.
"Systra will focus on demonstrating that it has not committed any offence," a spokesman for the company said Tuesday, adding that it will continue to operate as normal.
Two SNCF employees have already been charged with involuntary homicide over the crash.
Investigators confirmed SNCF's admission that the accident was the result of late breaking.
The spectacular November 14, 2015 crash -- which came just a day after the terror attacks that killed 130 in Paris -- happened when the train struck a bridge before jumping the track and breaking in two, landing partially in a canal.
At the time of the accident there were seven people in the driver's wagon, instead of the authorised four.