The origins of the name are uncertain. One claim is that the '99' was coined in Portobello, Scotland, in 1922, by the Arcari family, who owned a well known ice cream shop there. They sold ice-creams with half a large 'Flake' inserted in the top, and reputedly gave it the name simply because the shop was sited at 99 High Street. The idea spread locally, then further afield.
Another explanation for the name could refer to the last wave of conscripts for the First World War having been born in 1899 and referred to as "i Ragazzi del 99" - the Boys of '99. They were held in such high esteem that there are even streets in Italy named in honour of them after the War. If the 99 was launched in 1928 then possibly this was the reason why ice cream sellers in the UK were attracted to the name. It could well be that the chocolate flake reminded Italian ice-cream sellers (many of whom hailed from mountainous areas in the Veneto, Trentino, Bellunese and Friuli) of the famed Alpine Regiments - the Alpini - who wear a long dark-coloured feather cocked at an angle on their helmets.
A plain chocolate 99 Flake
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A plain chocolate 99 Flake
Yet another ingenious suggestion is that the initials of "Ice Cream", IC, form the Roman numerals for 99 (being 100 - 1). In practice, the number 99 is not written like this but as XCIX (wafer, chocolate, ice cream, wafer?). It could, of course, be that the name was coined by someone who either did not know this or ignored it.
One more explanation suggests that the original length of the flake chocolate bar was 99mm.
And, finally, a company known as "Askey's" first established a cone called "99". As people ordered this, "99 with a flake" would have been shortened over the years to "99 flake".
The Cadbury's website says that the reason behind the Flake being called a 99 has been "lost in the mists of time".