Passengers and members of the locomotive crew were not injured because they had been warned about the heightened threat in advance and evacuated promptly.
Ukrainian Railways said its monitoring center, which tracks aerial threats around the clock, alerted the train crew in time to begin the evacuation.
Emergency services and railway workers are operating at the site and dealing with the consequences of the attack.
Passengers were urged to closely follow announcements and comply with railway staff instructions while traveling.
The strike came two days after Russian forces twice attacked a passenger train in Odesa Oblast carrying around 600 people, including 15 children.
After the first strike on Aug. 23, Russian forces launched a second attack while rescuers and emergency services were already working at the scene.
All passengers and railway employees had been evacuated before the repeat strike, and no casualties were reported.