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.
"It is quite remarkable that the man is still alive," she said.
A spokesperson for freight carrier Cargolux confirmed in an email to Reuters that the stowaway had been on a flight operated by Cargolux Italia.
According to flight data, the only Cargolux freight flight from Johannesburg to Schiphol on Sunday also made a stop in Nairobi. It is not known if the man boarded the plane in South Africa or Kenya.