Defender Farrend Rawson, on loan from Derby County, played the full 90 minutes as the Millers beat Brighton 1-0 earlier this month.
The Football League said a football disciplinary commission will hear the case at the "earliest possible opportunity" so the matter is resolved before the end of the season.
Rotherham are 21st in the Championship.
United, who could have three points deducted, are currently seven points clear of the relegation zone.
Rawson joined the Millers on a 28-day youth loan on 7 March meaning his loan spell finished the day before the win over Brighton.
After that game boss Steve Evans said his loan had been extended until the end of the season.
But he was then left out of Saturday's 2-0 loss at Middlesbrough, and the Millers manager said Rawson had been recalled.
Divisional rivals Blackpool were fined £30,000 earlier this campaign after fielding an ineligible player in their defeat by Millwall.
Rotherham have been charged by the Football League with fielding an ineligible player.