The decision came only 10 days after Russia decided to halt its own train service to the Black Sea peninsula due to low ticket demand.
The joint decisions mean that most of the region's 2.3 million residents will only be able to reach mainland Ukraine by car or cross into Russia to the east using an outdated ferry service.
Some Russian carriers also continue to operate regular and charter flights to Crimea's central city Simferopol.
The European Union has slapped those operators with sanctions that deprive them of aircraft insurance and service contracts.
Ukraine's state railway operator did not explain what dangers its trains faced in Crimea.
The region was seized by Russian troops in March and later voted to secede from Ukraine in a hastily-arranged referendum that was denounced as illegal by Kiev and the West.
Its subsequent annexation by Moscow sparked the first of several waves of Western sanctions against Russia for its approach to Ukraine.