The physician, who helped care for Schumacher at the Grenoble hospital in France, recently visited the 45-year-old at his Switzerland home.
Schumacher, who was hospitalised for around six months after hitting his head while skiing off-piste in the French Alps in December, returned home to continue his rehabilitation in September, three months after he awoke from an induced coma.
Payen told RTL Radio that a three-year recovery process is possible, before adding: "Life after a head injury is punctuated by stages. We hope, but we have to give him time."
Schumacher, who has won seven world titles in his career, retired from Formula 1 in 2012.