The Amtrak train traveling between New York and Miami collided with the CSX freight train and derailed in Cayce, near Columbia, the state's capital, at around 2:30 am on Sunday.
Amtrak said in a statement that the lead engine derailed along with some passenger cars. Eight crew members and 139 passengers were on board.
The Lexington County Sheriff's Department confirmed all passengers had been evacuated from the Amtrak train. Officials added that although 5,000 gallons of fuel spilled following the crash, there was no danger to the public.
Speaking to CNN, passenger Derek Pettaway said he was traveling south from Philadelphia to Orlando in a sleeper cabin when he was awoken by the impact of the crash.
He added Amtrak staff evacuated passengers in a "really calm fashion."
It is not known how many people were traveling on the freight train, or whether one of the two trains was stationary at the time of the collision.
The Red Cross said it was responding and providing support to victims.
The accident comes days after another Amtrak train carrying several dozen Republican lawmakers including US House Speaker Paul Ryan collided with a garbage truck in Virginia, killing one person and causing six others, including a congressman, to need hospital treatment.