Tony Antonelli, a crew member on Space Shuttle Atlantis, visited a Kent school to mark the planting of the tree.
DNA tests proved the tree was a descendant of the one in Woolsthorpe, Lincolnshire, under which Sir Isaac Newton is said to have first pondered implications of gravity.
Tunbridge Wells Grammar School for Boys welcomed Antonelli, who took a piece of the original apple tree into space on the latest shuttle mission a few months ago.
Dr Chris Atkinson, EMR chief scientist, said: "It was great to make the connection between our DNA expertise, the scientific endeavour of NASA and one of the world's most pioneering scientists."
Antonelli was joined on his voyage by Piers Sellars, who went to school locally. The team docked with the International Space Station in a journey that involved 186 orbits of Earth, travelling 4,879,978 miles in 11 days.