The man was hit by a Brighton to London express train travelling at 80mph on 24 June 2014.
He was leading a team of 12 repairing cracks in the track when he was stuck on the right shoulder and thrown down an embankment near Redhill, Surrey.
Network Rail pleaded guilty to two breaches of health and safety law.
Rail inspector Tom Wake said: "Network Rail's planning of track maintenance work fell below legal standards, placing workers in unnecessary danger and causing an employee to suffer life-changing injuries."
Network Rail said it had since banned working while trains are running on that stretch of railway.
Its south east managing director, John Halsall, said: "Safety is our absolute priority and it is clear that we fell short in this instance."
Network Rail has been fined £800,000 for an accident which left a track worker with multiple serious injuries.