Paqueta has been charged with four breaches of FA rules in relation to his conduct in West Ham's Premier League matches against Leicester in November 2022, Aston Villa in March 2023, Leeds in May 2023 and Bournemouth in August 2023.
The 26-year-old has also been charged with two further breaches in respect of alleged failures to "comply pursuant to FA Rule F2".
Paqueta was interviewed by the FA in September and gave the English game's governing body access to his phone.
The FA investigation started after suspicious betting patterns surrounding Paqueta's booking for shoving Bournemouth's Illia Zabarnyi in the closing minutes of a 1-1 draw on the opening day of this season.
"West Ham United's Lucas Paqueta has been charged with misconduct in relation to alleged breaches of FA Rules E5 and F3," an FA statement said on Thursday.
"It's alleged that he 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."
Paqueta has until June 3 to respond to the charges, subject to any request for an extension to the deadline.
Writing on his Instagram page, Paqueta was quick to deny the charges.
"I am extremely surprised and upset that the FA has decided to charge me," he said.
"For nine months, I have co-operated 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. Due to the ongoing process, I will not be providing any further comment."
In their own statement, West Ham said: "The club acknowledges receipt of the FA charge received by Lucas Paqueta for alleged breaches of their Rules.
"Lucas categorically denies the breach and will continue to robustly defend his position.
"The club will continue to stand by and support the Player throughout the process and will make no further comment until the matter is concluded."
