The RFL's match review panel had been asked to review amateur video footage which showed a number of fights breaking out.
Seven players from Fryston and two from Keighley have been cited.
Keighley's Emmerson Whittel suffered a broken jaw, while the club alleges Josh Lynam was also bitten on the ear.
The charges range from Grade A, which carries a maximum one-match ban, to Grade F, which can see a player banned for eight matches or more.
Fryston's Steve Scott, the only player to be charged twice, faces two Grade F charges.
Keighley, from League One, England's third-tier competition, progressed to the Challenge Cup fourth round with a 50-32 win over Fryston - a side from the second tier of England's amateur game.
The RFL has also launched an investigation that will look at "events surrounding the fixture".
The match, a 'home' game for Fryston, was played at nearby Featherstone in West Yorkshire after consideration was given to reversing the tie and playing it at Keighley instead.
Keighley have also complained to the RFL about their off-field treatment before kick-off, as they allege players and members of staff were refused entry to the ground without a valid matchday ticket.
The Rugby Football League has charged nine players from Keighley Cougars and Fryston Warriors after a brawl during their Challenge Cup third round tie.