The Flake chocolate bar itself was first developed in 1920. An employee of Cadburys noted that when the excess from the moulds used to create other chocolate bars was drained off, it fell off in a stream and created folded chocolate with flaking properties. In 1930, Cadbury started producing a smaller version of the standard Flake bar especially for ice cream cones.These were marketed under the name 99 Flake and sold loose in boxes rather than individually wrapped like the traditional Flake.
The origins of the name are uncertain. One claim is that the '99' was coined in Portobello Scotland, in 1922, by the Arcari family, Rudi Arcari's father Stephen came up with the idea not long after opening the shop in 1922. He would break a large 'Flake" in half and stick it in an ice cream. A Cadbury's rep took this idea to his company. The rep asked Arcari what he called it, and he gave it the name 99 simply because the shop was sited at 99 Portobello High Street. The idea spread locally, then further afield.
Another possibility, generally discounted is that it was named by Italian ice-cream sellers (many of whom hailed from mountainous areas in the Veneto, Trentino, Bellunese and Friuli) in honour of the final wave of conscripts from the First World War, born in 1899 and referred to as "i Ragazzi del 99" - the Boys of '99. They were held in such high esteem that some streets in Italy were named in honour of them. The chocolate flake may have reminded them of the Alpine Regiment's hat, with a long dark feather cocked at an angle.
The Cadbury's website says that the reason behind the Flake being called a 99 has been "lost in the mists of time" although it also repeats an article from an old Cadbury works paper, which states the name came from the guard of the Italian king which consisted of 99 men and "subsequently anything really special or first class was known as 99