The duo are on loan from Championship sides Sheffield Wednesday and Charlton Athletic respectively, and neither have been given permission to play by their parent clubs.
Both have been regulars in the first-team since moving to Glanford Park, with Clarke the Iron's top scorer with seven goals.
Connor Jennings and Andy Barcham are the two most likely to come back into the side, although midfielder Damien Mozika could be on the bench for the first time this season after suffering an ankle injury in pre-season.
Gillnmgham will be without Charlie Allen and Joe Martin, both with long-term wrist injuries.
The League Two leaders are also without Robbie Findley, who has returned to parent club Nottingham Forest after a month-long loan.
But Martin Allen, the Gills boss, should welcome back striker Deon Burton from a knee problem.
Adam Birchall and Connor Essam are also back in contention after returning from loan spells at non-league sides Dartford and AFC Wimbledon respectively.