Courtois has emerged as the Blues' new first-choice goalkeeper after spending three loan stints with Atletico Madrid in Spain.
With Cech being forced to fight for his place at Stamford Bridge, there were suggestions that the shot-stopper would look for pastures new.
However, Cech has stayed put and Courtois extended his stay with Chelsea by signing a five-year deal.
"I don't think there is a problem," Mourinho said in this afternoon's press conference. "Petr is a very intelligent guy, he knows that Courtois is to stay a long time.
"What happened I think was something that was very much on the table and something that everyone would expect. Now we have Courtois under contact for five years and that's a good situation. I'm more than happy to have both in my team."
The 32-year-old has been a Chelsea player for 10 years.