The £12,500 fine was imposed by the FA over payments to two former players.
The punishment has come two years' after the FA were made aware of the allegations.
Jake Orrell and Myles Wright, who have now left the club, had their wages paid through a private football academy linked to Chesterfield FC.
The payments were in breach of the FA rule C1, which states that all payments to players must be recorded in the club's accounts.
The CFC Football Development School LTD was owned by the Chesterfield's former CEO Chris Turner, and ex non-league player Liam Sutcliffe.
Turner resigned as the academy director before it went into liquidation, but it owed almost £250,000.
It's been reported that liquidators are still chasing the club for money owed due to the academy venture.