The Israel international scored the only goal as the Seagulls beat Newcastle United 1-0 in a Premier League clash at the Amex Stadium on Sunday.
However, Hemed was later involved in a coming together with DeAndre Yedlin during the closing stages, appearing to stamp on the Magpies defender's leg.
An FA statement read: "Tomer Hemed has been charged for an alleged act of violent conduct which was not seen by the match officials but caught on video. He has until 6pm on Tuesday to respond to the charge."
According to Sky Sports News, Brighton club will be contesting the charge, which if proven could result in a three-match suspension for the striker.
Hemed faces the prospect of missing league fixtures with Arsenal, Everton and West Ham United respectively.