Sherif, 20, has not played for Everton's first team and spent last season on loan at third-tier sides Rotherham United and Port Vale.
"It is alleged that the player breached FA Rule E1.2 in respect of 61 bets placed on football matches between November 20th 2024 and February 12th 2026," the FA said in a statement.
"Martin Sherif has until Monday, August 17th to provide a response."
Sherif is the latest player to face betting-related charges after Ivan Toney received an eight-month suspension in 2023 for 232 breaches of the FA's betting rules.