Paqueta is said to have taken yellow cards on purpose to make money or to make others money.
The allegations stem around matches in 2022 and 2023, including games against Leicester City, Aston Villa, Leeds United, and Bournemouth.
An FA statement said: "It's alleged that he (Paqueta) directly sought to influence the progress, conduct, or any other aspect of, or occurrence in these matches by intentionally seeking to receive a card from the referee for the improper purpose of affecting the betting market in order for one or more persons to profit from betting."
"For nine months, I have cooperated with every step of their investigation and provided all the information I can. I deny all the charges in their entirety and will fight with every breath to clear my name," Paqueta stated in response.