
Action was brought against Alexander Ponosov after 12 PCs in his school based in the Ural mountains were found to be running illegal versions of Microsoft's Windows and Office software.
However, the head teacher said that the computers were bought from a sub-contractor and that he had no idea the software on them was fake.
Ponosov has received high-level backing in his fight, after President Vladimir Putin described the case as "utter nonsense".
Former Soviet leader Mikhail Gorbachev had also approached Microsoft co-founder Bill Gates to ask him to step in and help the headmaster.
Ponosov said that he had not yet paid the 5,000 rouble (A$232) fine and would appeal the case.
A Microsoft spokesman explained that the case had been brought by the Russian authorities and that Microsoft had no plans to bring any proceedings against the man.
Copied versions of Microsoft software sell for as little as £3 (A$7) at markets in Moscow.