Derby magistrates fined Rosemary Robinson £3000 and ordered her to pay £350 costs after she pleaded guilty to operating without a licence at her shop, Food for Thought, in the city.
The licensing scheme was announced by FSA chairman Sir John Krebs immediately after the Agency was formed in April 2000.
It was a key recommendation of the public inquiry chaired by Professor Hugh Pennington into the E.coli 0157 outbreak which killed 17 people and made 500 ill in Lanarkshire, Scotland.
The new law came into force in November last year and applies to shops selling raw meat and ready-to-eat food to the public. A parallel scheme came into force in Scotland a month earlier.
FSA Director of Enforcement and Food Standards David Statham said after the court hearing: 'This prosecution shows that the licensing scheme is more than just a paper exercise.
'There are real safety benefits for consumers from the new regime - improved controls on hygiene and a more structured approach to training.
'It is right that if someone refuses to comply with these important new standards local authorities take appropriate action.'
Derby City Council chief environmental health officer Andrew Hopkin said: 'We did what we could to help Mrs Robinson. The prosecution was a last resort.'