The Portugal international is braced for the reality of being benched for the Blancos' Champions League game next week against Galatasaray, but says Mourinho knows best.
The 30-year-old has seen his appearances for the Spanish giant reduced in recent months, following setbacks from injury and the emergence of young starlet Raphael Varane.
Despite lining up against Zaragoza on Saturday, Pepe believes Varane - who did not travel - was conspicuous by his absence, and expects the Frenchman to be given the nod for the visit of the Turkish champion.
"I wouldn't be surprised if I wasn't selected, but I'm here for the team," Pepe said to Marca.
"The coach decides what is best. We have a good squad and, as I said before, I'm here to help. I've played many games for Real Madrid and my approach will be the same as always."
Pepe has featured in all of Madrid's eight games in the Champions League so far this season.