Zambezi, the male rhino, was being kept at the Port Lympne Reserve in Kent ahead of his transfer back to the wild as part of a programme to repopulate the Serengeti.
He was travelling with a team from the Grumeti Fund Reserve, alongside one of his dedicated keepers and a vet from Africa.
An investigation into his cause of death will be carried out "as soon as possible," according to the Aspinall Foundation - a British charity working to promote wildlife conservation.
A spokesman for the foundation said the movement of large animals and rhino in particular is not uncommon, reports Kent Live.
He said: "Nineteen black rhinos have been successfully moved from Europe by air to safe havens around the world, in the last few years.
"The Aspinall Foundation itself has already successfully translocated eight black rhinos to Africa from its Kent wild animal parks, which has assisted in boosting the dwindling population of black rhino that are registered as critically endangered in the wild.
"In addition, these rhinos have successfully mated and are responsible for the birth of at least 15 calves in the last 24 years."
Damian Aspinall, chairman of The Aspinall Foundation, said: "Sadly Zambezi passed away on the plane on his way to the Grumeti Reserve in Tanzania.
"Like everyone at The Aspinall Foundation, I am shocked and devastated by the loss.
"We do not yet know what caused his death, but we will, of course, carry out every examination and enquiry possible to see if there are lessons to be learned.
"The work of our foundation in breeding critically endangered species and returning as many as possible to protected areas in the wild will continue. Overall, we have been hugely successful.
"It is my firm belief that these animals do not belong in captivity. Our long-term goal is to see all zoos phased out or, if they’re not, to see them truly doing conservation work.
"Thank you all for your continued support of us and the critical work we do."