The deceased "adolescent black male, possibly of African origin" turned up during a "detailed post-flight inspection" of the C-130 at Ramstein Air Base on Sunday night, according to Pentagon Press Secretary Navy Rear Admiral John Kirby.
The body did not affect the plane's flight, nor was it visible during "standard" inspections before and after flights, he said yesterday.
He said it is not known when or where the stowaway entered the landing gear wheel well.
"The cause of death, as well as the other circumstances surrounding this incident, remains under investigation," Kirby said.
He said the body had been turned over to German authorities for autopsy.
The C-130 was "supporting Africa Command operations" during its various stops, he said.