He is accused of breaching the FA's Rule E8 (b) which prohibits players from betting on matches or competitions in which they are participating or have an influence.
The 21-year-old winger, who spent time on loan at QPR during their relegation campaign, has also withdrawn from England's squad for the European Under-21 Championship. He will be replaced in the squad by Birmingham's Nathan Redmond.
"The FA has announced it has charged Andros Townsend in relation to alleged breaches of its rules governing misconduct and betting," the FA said in a statement.
"The Tottenham Hotspur player has been charged with breaches of Rule E8 (b) in relation to a number of betting offences.
"The player has until 3 June to respond to the charges."
A separate statement from the FA said: "Townsend will receive the full support of the FA and Tottenham Hotspur FC in seeking rehabilitation whilst responding to the allegations."
The FA also announced Southampton left-back Luke Shaw had withdrawn from the England Under-21 squad to be replaced by Liverpool's Jack Robinson.