South Western Ambulance Service said it did not know how the incident involving the man - thought to be in his 20s - happened.
Great Western Air Ambulance flew him to Queen Elizabeth hospital in Birmingham after the ambulance service was called at about 17:10 BST.
Wiltshire Air Ambulance had also been called after the man suffered significant burns at the Somerset site.
Final preparations are taking place for the 2016 edition of the festival which opens its doors to the public on Wednesday.
A man has suffered severe burns at the Glastonbury Festival site.