Flights from Johannesburg to Amsterdam take about 11 hours, with the cargo plane believed to have made one stop, in Nairobi, Kenya.
It is very unusual for stowaways on long flights to survive, due to the cold and low oxygen at high altitudes.
The man's age and nationality have not yet been determined, police say.
"The man was found alive in the nose wheel section of the plane and was taken to hospital in a stable condition," Royal Dutch Military Police spokeswoman Joanna Helmonds told the AFP news agency.
