Portsmouth won the cup final 1 - 0 and even though City won at Fratton Park at the start of this season McNaughton wants to beat them some more.
"There is always a score to settle with Portsmouth," said McNaughton.
But now the focus is on league action and the realism that cardiff are just five games from promotion to the Premier league.
"In some ways Saturday's game is more important for us." he continued. "It took a while for me to watch that FA Cup final again because it did hurt a lot. I thought they were there for the taking but we didn't have enough on the day.
"So there is a bit more incentive on the game on Saturday.
"But while cup finals were great for us, it was just a bonus to get there.
"In terms in pushing this club onwards it would be an unbelievable step for this club to get into the Premier League.
"So it would be great to secure a victory to keep our run going and keep our spirits up for the QPR game."
Cardiff will keep second place if they pick up three points against a Pompey side looking to recover from a 3 - 0 home defeat by Coventry City in midweek.