The Belgium goalkeeper says beating Barcelona would be more satisfying should the Argentine play a part in the crucial top-of-the-table clash on Saturday
The Argentine made his comeback from injury against Getafe in midweek, scoring twice in a brilliant 30-minute cameo, although he is likely to start from the bench once more in the clash at Vicente Calderon.
Courtois admits he finds it easier to sleep knowing Messi and Neymar - who is struggling with a virus - will not both feature from the start on Saturday, but the Belgian maintains it is more satisfying to win a game where he has faced an opponent of the calibre of Messi or Cristiano Ronaldo.
"I don't fear them. You always try to give your best against them," he told AS. "They are great players, different from each other, and it's always good to play against them, because if you win it has more value.
"Of course [it's better knowing Messi and Neymar won't start]. After his injury, Messi came back well. I think he's among the best in the world, or the best. He's always dangerous, but we will try to stop him and Barcelona.
"Neymar is becoming more and more important for Barca. He is a great player and we have to analyse him to find a way to stop him."
Atletico head into the encounter level on points with Barca at the top of La Liga, but Courtois maintains their early-season form will count for nothing if they allow their standards to slip in 2014.
"The match against Malaga was very difficult but in the end we won and got the three points. We hope to do the same against Barcelona, but we know it's a tough game," he continued.
"Perhaps Barca are favourites, but we are joint-leaders and we want to win and take the points.
"For us, every game we play is a final, and this is one more. Being winter champions is something for the record books, it doesn't help us win the title.
"If you're up there at the end of the season you can talk about being champions. If not, you can't.
"In those two games [in the Supercopa] they were adapting to the new system under Martino. Recently, they've been playing pretty well.
"If we win it would be a major victory. We've won against Madrid this season and to win against Barca would be great, but the season is very long."
Finally, Courtois admitted he was pleased to hear Atletico are keen to make his loan move from Chelsea permanent, but stressed he is yet to hold talks with the clubs about his long-term future.
"There are still things to talk about and when the time has come to say what I will do, I will. But, in truth, I don't need to speak about this now," added the 21-year-old.
"My agent will talk to Chelsea first, and then I will. But for now there are a lot of games and I want to concentrate solely on that.
"I have great confidence in Atletico [about signing me]. But first there are things I need to discuss with everyone.
"I've won titles and grown a lot as a goalkeeper here. I've become the keeper I am today thanks to Atletico."