The FA said in a statement that it was alleged the 26-year-old, who was charged with misconduct, breached the rules 232 times between 2017 and 2021. Toney has until Nov. 24 to respond the charges.
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."
After the newspaper report was published, Toney said he was assisting the FA with its enquiries.