The East Midlands Trains service was travelling at 65mph (105 km/h) when it derailed at Barrow on Soar in Leicestershire in February 2008.
The train derailed after an engineering works tipper lorry hit a footbridge.
Leicester Crown Court heard the firm did not have a proper construction site safety assessment in place.
A train driver had to be cut free from his cab after the bridge collapsed in the accident, but no-one else was hurt.
A warning message had been sent out, but the Nottingham-to-Norwich passenger train was unable to stop in time.
The tipper truck driver did not realise the height of his truck and had left the back of it raised in the air, the court heard.
The train driver was trapped for two-and-a-half hours and suffered serious leg injuries.
"Network Rail's poor planning and management of construction site safety at Barrow placed members of the travelling public a risk," Darren Anderson of the Office of Rail Regulation said.
The court heard that the train driver "thought he would die" and still suffered from flashbacks.
"It should never have happened and I would like to say sorry for the fact that it did happen," Network Rail spokesman Martin Frobisher said.
Network Rail has been fined £80,000 and ordered to pay costs of £32,000 after admitting causing a train to derail in Leicestershire.