Captain Flinders led the first circumnavigation of Australia and is credited with naming the country.
Some 61,000 skeletons will be removed from St James's Gardens, where the station for the HS2 rail route will be built near London Euston station.
A recently discovered coffin showed the captain was buried on 23 July 1814.
The dig began in October - one of 60 archaeological sites between London and Birmingham being explored prior to the construction of the £55bn high-speed rail line.
It was known Captain Flinders was among the thousands of people buried at the site, which was built over when Euston station was expanded in the 19th Century but it was unclear whether his body or others would be able to be identified.
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