William joined pilots, ground crew and families from 29 (Reserve) Squadron in Lincolnshire, which is also celebrating its 100th anniversary.
The squadron trains Typhoon jet pilots, and the base is home to the Battle of Britain Memorial Flight (BBMF).
Prince William took to the skies in a Chipmunk as part of the event.
He had been due to fly in a Dakota belonging to the BBMF, but the aircraft had a problem with one of its engines.
Sqn Ldr Martin Morris explained: "It is a very old aircraft and we couldn't get one of the engines up to its full operating speed - so he got to fly in a Chipmunk instead."
He said about operating the BBMF's historic aircraft: "Anything to do with aviation has got to be safety related. If there is any doubt, there is no doubt."
After his flight, piloted by Sqn Ldr Duncan Mason, Prince William joked: "For a beginner, he was alright."
The Chipmunk was joined in mid-air by a BBMF Spitfire.
Sqn Ldr Morris said about the royal visit: "With it being the 75th anniversary of the Battle of Britain - a very special year - in many respects this is the icing on the cake.
"It is the acknowledgment and recognition of what the veterans did, as part of 'the few', during the Battle of Britain."
1,023
aircraft lost by RAF
1,887
aircraft lost by Luftwaffe
3,000 aircrew served with RAF Fighter Command
20% were from the British Dominions and occupied European or neutral countries
544 RAF Fighter Command pilots were killed
2,500 Luftwaffe aircrew were killed
The Battle of Britain was the German air force's attempt to gain air superiority over the RAF.
Their ultimate failure was one of the turning points of the Second World War and prevented Germany from invading Britain.
The Duke of Cambridge has flown with crew from RAF Coningsby as part of commemorations to mark the 75th anniversary of the Battle of Britain.