They will then plot a course over The Mall and Buckingham Palace at 1pm before heading West.
The Queen, The Prince of Wales, The Duchess of Cornwall and other members of the Royal Family will watch from the Palace while thousands are expected to line the Mall.
Heathrow Airport will close for 20 minutes as planes then split up to head towards Hendon, Runnymede, Windsor and Maidenhead.
A large area of airspace above the capital and surrounding areas, including the Norfolk coast, Colchester and Ipswich, will be restricted and used only by the aircraft taking part.
More than 11 months in the planning, the display will involve aircraft representing the whole of the RAF throughout the years, culminating with the Red Arrows bringing the flypast to a spectacular end.
Where can I watch the flypast?
The planes will take off just south of Ipswich at 12.45pm before passing over Colchester, Witham and Chelmsford then swooping through East London.
Anyone hoping for the best view should make their way to the Mall leading up to Buckingham Palace, where the flypast will take place overhead at 1pm.
Those not in the South East can watch live coverage on BBC One or stream on BBC iPlayer to watch the events as they unfold live.
The programme begins at 9.30am until 1.20pm
The RAF said: "It promises to be a spectacle never seen before and one that won’t be seen again for a very long time."
Alternatively you can listen to BBC Radio 2 for further coverage.
Suffolk
The flypast will begin south of Ipswich, where the planes will gather to form the 100-strong assembly.
It will then head towards London, so if you live in the South of the county then keep your eyes in the sky from 12.45pm.
Essex
The flypast will head over Colchester, Witham and Chelmsford before swooping into East London.
Do you live in any of these towns or areas? Then it's likely you'll be able to witness the spectacle.
The Mall
A special parade will march through The Mall in front of Buckingham Palace this morning at 11.25am as festivities get underway.
The flypast is due to arrive at The Mall at around 1pm — finished off by a red, white and blue smoke-tail from the famous Red Arrows.
London Southbank
Any position around the Thames in Central London should give you a prime view of the flypast.
Among the best positions will be around Waterloo Bridge on the Southbank.
Victoria Park
The planes will be arriving from East London, meaning a clear space away from tall buildings.
That makes Victoria Park a prime location to marvel at the flypast.
Wimbledon
The planes will head westward after passing over Buckingham Palace at 1pm.
It means they will pass near Wimbledon, giving tennis spectators a chance to join in the celebration.
Surrey
The planes will splinter off into different directions after leaving West London.
It means many will still get an opportunity to see at least part of the 100-strong flypast.
They will head towards Heathrow, Runnymede, Windsor, Maidenhead and Hendon - so if you live in any of these areas then keep your eyes peeled.
The cutting-edge stealth fighter F-35 jets are expected to feature - as are helicopters including the Puma, Chinook, Juno and Jupiter.
Jets from the Battle of Britain Memorial Flight - the Dakota, Lancaster, Hurricane and Spitfire - will also be taking part.
They will be joined by the Hercules, Atlas A400M, C-17, BAe 146, Sentinel, Voyager, Shadow, Rivet Joint, E-3D Sentry, Tornado GR4, Typhoon and Red Arrows.
Lancaster bomber and Red Arrows take to the sky on Armed Forces Day as PM Theresa May and Princess Anne attend Llandudno ceremony
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