The claim covers 14.6 million hectares of land, a larger area than all of England, taking in all of the areas of the Cape not already under native title as well as some inland waters.
The Cape York Land Council lodged the claim on Thursday on behalf of nine traditional owners. If finalised - a process expected to take several years - it will mean that all significant activity, including mining and development, will require consent from traditional owners.
'This means the traditional owners of the Cape will be the real masters of development and use of their lands,' Cape York Land Council chair Richie Ah Mat said in a statement.
Indigenous people will be able to reconnect with country as well as grow the local economy, reducing welfare dependency, he says.
Mr Ah Mat says individual groups will still have a say over their land.
Olkola elder Mike Ross, one of the claimants, says it will allow Aboriginal people to make decisions over their ancestral lands.
'Coupled with the transfer of freehold, this native title claim makes our historic ties to the land clear,' he said, adding that the region was under pressure from miners and other interest groups.
Mr Ross, who is the chairman of the Olkola Aboriginal Corporation, was in Cooktown this week to celebrate the transfer of more than 600,000 hectares of Cape York pastoral land back to his people.
It's hoped that by lodging a single claim for Cape York the native title process, which in some cases has taken decades to finalise, will be resolved within a few years.
The Cape York Land Council says it has undertaken extensive consultation and will continue to work with traditional owners.