The Seleccao center back says that it is "not normal" that his compatriot has only lifted the trophy on one occasion in light of the forward's remarkable statistics.
The 28-year-old attacker was awarded the trophy in 2008, while he also made the podium in 2007, 2009, 2011 and 2012.
However, Pepe believes his compatriot has not been given enough recognition and suggested that FIFA president Sepp Blatter's recent revelation that he favors Lionel Messi over Ronaldo was telling in that regard.
"We know that, even just for the figures Cristiano has racked up, it’s not normal that he’s only won the Ballon d’Or once after being to the gala seven or eight times," the defender told AS. "It just shows that a lot of strange things happen in football. It’s not fair what has happened to Cristiano.
"I hope he wins the Ballon d’Or. Blatter’s comments have been a real eye opener for a lot of people. What Cristiano does is beyond compare. He has an unbelievable record and he’s the best player on the planet. As I say, you cannot compare him to anyone right now."
Ronaldo has been in sublime form this season, netting 24 goals in 17 appearances for Real Madrid.