The 51-year-old from Kirkby, who has asked not to be named, suffered fractures to his spine, breastbone and ribs in the incident at St Marys Primary School, and narrowly avoided being paralysed.
St Helens-based W Swindells & Son (Roofing) Ltd was prosecuted by the HSE after an investigation found the firm had failed to put measures in place to prevent workers falling through skylights.
Leyland Magistrates’ Court was told that the firm had been hired to replace the roof on the school on Hornchurch Drive in Chorley.
The skylights had been removed and the roof felted over, before another team was sent up to install new tiles.
The worker stepped backwards onto the unsupported felt over a skylight hole and fell three metres to the floor below, striking a partition wall as he fell.
He was in hospital for two months and will never be able to return to work due to the extent of his injuries. His wife has also had to give up work to care for him.
The court heard his injuries could have been avoided if Swindells had planned the work properly and arranged for pieces of plywood to be put over the skylight holes.
W Swindells & Son (Roofing) Ltd, of Hill School Road in St Helens, was fined £4,000 and ordered to pay £3,153 in costs after pleading guilty to a safety breach.
Speaking after the hearing, HSE Inspector Chris Hatton said: “The worker could easily have been killed when he fell through the roof and will be affected by his injuries for the rest of his life.
“If the company had taken the simple measure of fitting pieces of plywood over the holes then his injuries could have been avoided, but it failed to properly plan the work and anticipate the dangers.”