Thirty-seven of the 123-car Burlington Northern Santa Fe empty train left the tracks in Dewey, Custer County, at about 2.30am Monday on its way from Wyoming to Nebraska.
No injuries were reported in the incident.
BNSF spokesperson Amy McBeth told the Rapid City Journal earlier this week that both of the two sets of tracks the company maintains from the Wyoming coal fields to southwestern South Dakota had suffered damage.
Track repair and debris clean-up have now been completed.