Thomas Cowell was droving cattle in South Australia's far north when he was found dead at Kopperamanna Bore in March 1959, aged about 65.
Police were called and buried the Lower Southern Arrernte man at a nearby dam but in 1966, his grave site was disturbed by flooding and police returned to collect his remains.
Officers could not locate any family and sent the remains to the South Australian Museum.
Documents indicated Mr Cowell was a worker at Mt Dare Station.
Elders recently helped identify extended family who were notified and requested Mr Cowell be returned to Country for burial within the Witjira National Park near Mt Dare.
Mr Cowell's remains will be collected in Adelaide on Monday and driven to the reburial site where family, community, police and SA Museum representatives will camp overnight.
His reburial ceremony will take place on Thursday during National Reconciliation Week.
SA Museum Aboriginal Heritage and Repatriation Manager Anna Russo said the museum had a program to progressively return thousands of Aboriginal remains collected from the 1870s through to the 1980s.
"Over the last few years, we've been working with communities to return their ancestors back to Country and burial, so that number is coming down," she told AAP.
Now-obsolete instructions from the Commissioner of Crown Lands meant any Aboriginal remains found or dug up through public works had to go to the SA Museum.
"It goes back to those racist theories around evolution and pseudoscience, people thinking they could measure and do scientific studies on the remains of Aboriginal people," Ms Russo said.
It was estimated about 10,000 Aboriginal remains were collected by museums across Australia, with the SA Museum accounting for about half of them, she said.
SA Aboriginal Affairs Minister Kyam Maher said Mr Cowley had been lost to the community for a long time
"It means a great deal that the South Australian Museum has consulted his family and worked hard to return him to Country," he said in a statement.
The South Australian Museum participates in the federal government's Indigenous Repatriation Program, funded by the Commonwealth Office for the Arts.