The exact meaning of magistrate varies widely depending upon the context. For example:
in the U.S. federal court: assists district court judges by handling minor offenses or administrative tasks such as preliminary hearings (often referred to as a magistrate judge rather than just a magistrate)
in some U.S. states: a judge in the state court
in France, Belgium, Italy, the Netherlands, and other civil law countries: a sitting magistrate is a judge and a standing magistrate is a prosecutor
in England: may be a volunteer without formal legal training who performs a judicial role with regard to minor matters
in ancient Rome: a powerful officer with both judicial and executive power
Frederick, it was said, intended to bring against them twenty men all armed with guns, and he had already bribed the magistrates and police, so that if he could once get hold of the title-deeds of Animal Farm they would ask no questions.
There are no more uses of "magistrate" in Animal Farm.