The Scottish Football Association's compliance officer Vincent Lunny has on Tuesday written to the cash-strapped Fife outfit ordering them to appear before a Hampden hearing later this month.
The Pars hosted Hamilton at East End Park on February 2 but lost the fifth-round tie 2-0.
The club are now accused of breaching Scottish Cup rule 46 (c)(3) that says ticket money, after the deduction of expenses, should be shared evenly between clubs.
They also face a charge relating to a breach of cup competition rule 46 (e) which instructs that "the share of the receipts, or the guarantee, should be paid, in cash, on the day of the match, unless any agreement is made to the contrary".
Dunfermline's case will be heard at Hampden on Thursday, March 21.
This is the latest cash crisis to hit the club after it was announced Dunfermline had paid their players just 20% of their February wages, prompting the Professional Footballers' Association Scotland to last week lodge a formal complaint with the Scottish Football League.