Parkinson faces the dilemma of disappointing several members of his squad that have helped the League Two club reach Wembley, and the Bantams boss has admitted that he can do little more than be honest with his players.
The 45-year-old told reporters: "I've got a couple of players who've had injuries and I face some massive decisions.
"It's been a squad effort to get here. Without a doubt, leaving people out for a game of this magnitude will be the worst part of my job this week.
"I can only make the call honestly and explain the reasons why to a player. It's a situation you've got to handle the right way."
Bradford qualified for Sunday's showpiece by seeing off the challenge of Aston Villa in the semi-finals.