Charlton said: “We’ve had four games in 12 days and seven in the last 25. We’re down to the bare bones and there’ll be a few young lads in the team on Thursday.
“It’s certainly taken its toll on us. There’s just nothing left in the tank of a lot of these guys and I can understand why.
“We did all right for 60 minutes against Barrow, but I understand how we’re fatigued in the last 20 minutes and I think everybody else does too.”
He added: “York have got everything to play for and we’ve just got to give it our all.”
Knights coach Gary Thornton remains optimistic as his side battle to avoid the drop.
York are three points adrift at the bottom of the table but have a game in hand on the teams around them.
Thornton said: “We’ve got three games left and three wins are possible. We’ve got to give it a go.”