The 28-year-old has been charged with betting on a total of 150 football matches, breaching rule 33, which forbids players from gambling on games of their registered club or indeed, on any football match.
The charge does not allege that Moffat made bets against his own team.
The player will have his case heard by a judicial panel on January 16.
The bets Moffat is alleged to have placed involving the Honest Men took place between August 3, 2012 and August 10 this year.
Between February 19, 2012 and September 1, 2013 he allegedly bet on 150 football matches.
In September, Rangers midfielder Ian Black was issued with a censure after admitting betting on 147 football matches.
The former Inverness and Hearts man was also given a 10-match ban, of which seven games were suspended, after admitting betting on matches involving his own team. Three of the bets concerned were on his club not to win.
Rule 33 states that "no club, official, Team Official or other member of Team Staff, player, match official or other person under the jurisdiction of the Scottish FA shall bet in any way on a football match (except authorised and registered football pools)."