"Replays probably gives the bigger clubs an advantage. They've got more of a chance to turn round their squad."
The First Division side face Aberdeen on Tuesday night in their Scottish Cup fifth-round replay at Pittodrie, after the first match ended 1-1.
McGlynn is looking for a reaction from his players after a 4-0 home defeat to Inverness Caledonian Thistle in the league on Saturday.
"Confidence is a big thing in football. You get confidence from winning, but it gets dented from losing games," he told BBC Scotland.
"This is a cup tie, a big game and we seem to rise to that challenge."
It was the First Division side who looked like progressing to the Scottish Cup quarter-finals in the original game at Stark's Park, but Gary McDonald's 95th minute leveller for the Dons put paid to a shock.
"We did fairly well in the first game and we believe we can do equally as well in the replay," said McGlynn.
"Of course we are the underdogs, but that brings more pressure to Aberdeen because they're expected to win the game."
McGlynn believes Raith have to avoid conceding an early goal if they are to have a chance of knocking out the Scottish Premier League team at the second attempt.
"We have to go there, make them a bit nervous, create a couple of chances and get their fans turning on them," he added.
"The longer it goes 0-0, then hopefully we can take it all the way to the wire.
"It's like Aberdeen going to Rangers or Celtic - they wouldn't want to lose an early goal there."
Source: BBC Sport
Source: BBC Sport