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."

The two-year-old was talking to the two teenagers as her mother shopped nearby when she was snatched.
She was found an hour and 45 minutes later in a park three miles away and the girls, 13 and 14, were arrested.
The pair were ordered to be detained for three years and the mother said she hoped they would get help and lead worthwhile lives when released.
The woman, who is not being named to protect her daughter's identity, said: "It all happened within the blink of an eye - we think we are careful, but honestly we are never careful enough.
"All it takes is for a child to run off or run around a corner and you trying to keep up and everything changes.
"My little one was laughing and running up and down in the store and I could hear her voice but then I couldn't. I knew something was wrong because she always likes me in her sight."
Speaking to BBC Newcastle, the mother said that when police brought her child back to Primark, she realised she had been targeted deliberately and the kidnapping had not been a spur-of-the-moment thing.
She said her daughter's hairstyle had been changed and she was sucking a baby bottle the girls had bought.
"I was very, very frightened - it was completely numbing - the last thing you expect," she said. "These are kids, what were they thinking?
"It was an evil act, but would I call them evil? No."
During sentencing of the pair in July, Newcastle Crown Court heard how they had carried out online searches on topics such as rape and children having sex.
Mr Justice Globe said although their victim was not harmed there had been intent. He detained the girls, who cannot be named due to their age, for three years and three months.
They were initially charged with kidnap with the intention of committing a sexual offence but this was dropped.
16:30 - Child taken from Primark store in Northumberland Street
16:35 - Girls go to nearby Metro station and travel to Gosforth
16:55 - CCTV from store's exit identifies kidnappers, every police officer in Newcastle alerted
17:00 - Teenagers shoplift baby milk and bottle from Sainsbury's store in Gosforth
18:01 - The three are spotted at Gosforth Park and the teenagers are arrested
The mother said parents needed to monitor older children more closely.
She said: "Parents need to find ways to get to their teenagers - we all know that teenage life is difficult - we don't know what children are doing online or who they are communicating with, so I plead with every parent to take every precaution to keep the little ones and the teenagers safe."
She added: "But who am I not to forgive them? One of the biggest problems in the world is our inability to forgive one another.
"She was not harmed in any way and has no recollection of that day."
Network Rail has been fined £800,000 for an accident which left a track worker with multiple serious injuries.
[NEXT_CONCEPT]
The mother of a toddler who was taken from Newcastle's Primark store says she has forgiven the girl's kidnappers.