The private bus, which was empty except for the driver and broke up into pieces following the impact of the collision, was crossing the track between the Ajayabpur and Dankaur railway stations around 4.50 a.m.
The bus driver found the rail-crossing gate open and attempted to drive across to the other side when he saw the Gorakhdam Express, coming from Gorakhpur to Delhi, speeding towards him, said Anil Kumar Gautam, station officer of Government Railway Police at Aligarh railway station.
The driver jumped off the bus and managed to flee just before the speeding train rammed into the vehicle.
The rail-crossing gateman was critically injured and about half-a-dozen people sustained minor injuries.
Officials said the movement of about 35 trains, including the Lucknow-bound Shatabdi and the Kolkata-bound Rajdhani, were disrupted for about five hours.
According to Gautam, the private bus was trying to cross over to fill CNG when the engine developed a fault and the vehicle stalled in the middle of the rail track.
Due to the impact, the bus was hurled into the air and broke up into pieces. The train engine also derailed, disrupting movement of trains on the track. Train movement could be restored only after the third track was opened after repairs.