A report in the Daily Mail newspaper this month said Toney had been under investigation for around seven months in relation to the alleged betting activity before he played for Brentford.
It added there were no suggestions that he had betted on his own team to lose matches.
"Brentford has been informed that Ivan Toney has been charged with breaches of FA Rule E8," Brentford said in a statement.
"The club has been in discussion with Ivan and his legal representatives about this matter and those conversations will continue privately. We will make no further comment until the matter has been completed."Tyson Walker Jersey
After the newspaper report was published, Toney said he was assisting the FA with its enquiries.
He was not named in Gareth Southgate's England squad for the World Cup in Qatar which begins on Sunday.