Traveling by rail continued to happen during the Khmer Rouge regime. A large scale relocation of people occurred for the second time, after the fall of Phnom Penh on April 17, 1975. About half a million people were forced to evacuate for a second time to the northwestern part of Cambodia and this happened via train travel between late 1975 and 1977.

Even in the last minutes of Democratic Kampuchea rule, senior Khmer Rouge leaders escaped using the railway that connects to Cambodian-Thai border as the Vietnamese troops entered the country on January 7, 1979.

The passenger trains stopped service in 2003 due to aging and fragile conditions from the war. The rail line leading to Sihanoukville resumed its passenger services in 2016 and the one continuing to the Cambodian-Thai border was restored in 2018.