The accident happened at a house in Medinah Close, Collingtree Park.
Warwickshire and Northamptonshire Air Ambulance said the men were both at the top of the scaffolding and fell from a height of up to 15 metres.
The charity was called to the scene at about 1.45pm on Friday and used their helicopter and rapid response land vehicle to get to the patients.
One patient, a 55-year old man, sustained serious chest injuries as well as a potential head injury.
Due to the nature of his injuries, he was anaesthetised and given emergency surgery to help with breathing.
He was immobilised and quickly airlifted to University Hospitals Coventry & Warwickshire, where he arrived at about 3pm, for further treatment.
The second patient, a 42-year old man, sustained injuries to his lower back. He was given advanced pain relief and immobilised before being taken by land ambulance to the same hospital.