The Holigost - or Holy Ghost - was one of four "great ships" commissioned by the king in his war against France.
It was spotted in an aerial photograph by historian Dr Ian Friel, in an area of Hampshire's River Hamble described as a medieval breaker's yard.
Historic England said it was a "tangible link" to Henry V.
The Holigost fought in sea battles during the Hundred Years War which broke the French naval power.
Dr Friel identified the wreck when he was revisiting documentary evidence for a book on Henry's navy.
Future scientific research on the ship, which could include sonar and aerial imaging using drones, could reveal much about 15th Century shipbuilding and improve understanding of life aboard ship, naval warfare of the time, dock building and docking practices.
Historic England said it was taking steps to protect and investigate the shipwreck in part of the river next to where Henry's flagship, the Grace Dieu, was identified in the 1930s.
Duncan Wilson, Historic England's chief executive, said the investigation in the 600th anniversary year of the Battle of Agincourt, was "immensely exciting."
"It holds the possibility of fascinating revelations in the months and years to come," he added.
Dr Friel said: "In my opinion, further research leading to the rediscovery of the Holigost would be even more important than the identification of the Grace Dieu in the 1930s.
"The Holigost fought in two of the most significant naval battles of the Hundred Years War, battles that opened the way for the English conquest of northern France."

There were 108 inward investment projects counted in the 2015-16 financial year.
In the previous two years, there were 122 and 119.
The number of jobs created was well below a proportionate share of the British jobs, at 4,200.
The British numbers had another strong showing in both projects and jobs supported.
Foreign investment in the UK reached more than 2,200 projects, up 11%.
This Whitehall report says nearly 83,000 jobs were created that way, down slightly, but the second highest since the data began.
The projects counted in these figures included new factories and branch offices, expansion of existing plants, and firms being taken over.
The sectors most affected were in finance, professional services, and manufacturing.
Although London dominates, with 889 projects attracted last year, Scotland is rated as being attractive to foreign investors.
In a separate annual survey by the business consultancy EY, it has recently come second, after London.
It has been helped by the experience built up in Scottish Enterprise and the government agency Scottish Development International. By contrast, in recent years, English regions' efforts have had to adapt to the dismantling of regional development agencies.
They may now be catching up. Northern England saw 228 new projects in 2015-16, a rise of 24%, linked to 10,700 jobs. Wales secured 97 projects, with 5,400 jobs attached.
Commenting on the most recent figures, International Trade Secretary Dr Liam Fox said they show "the UK continues to be the place to do business".
He added: "We've broadened our reach with emerging markets across the world to cement our position as the number one destination in Europe for investment.
"This continued vote of confidence in the UK will help attract foreign investment to create jobs, security and opportunities for people across the UK."
The UK government report does not say why Scotland's share of projects and jobs created has fallen.
But among possible explanations: the competition from England is getting tougher, the slump in oil and gas has hit Scottish numbers, and investors may be discouraged by political uncertainty.
We never know how many potential projects go elsewhere, because it's very rare for a foreign company to announce which options it has rejected.
With political and economic uncertainty resulting from the European Union referendum, a key test of the UK government and its trade secretary Dr Liam Fox will be how well inward investment performs in 2016-17 and beyond.
One of the main reasons given for locating factories and offices in the UK has been its access to the European Union's single market, and it is far from clear whether that will be retained after the UK leaves.
The wreck of a 600-year-old warship which helped Henry V wage war on France is believed to have been found buried in a river.
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Scotland's share of inward investment projects has fallen, according to the latest figures from the new UK Department for International Trade.