The 55-year-old actor's co-star Gillian Anderson was reportedly offered less money to reprise her role as Agent Dana Scully on the latest series.
However, Duchovny said he did everything he could to ensure his co-star was paid the same, reported The Guardian.
"I've done everything I can to help that whenever I could. I think we should be paid the same to do 'The X-Files'," Duchovny said.
"You can ask Gillian. She knows that I have always wanted us to be paid the same, for as long as I've known there was a discrepancy. Hollywood payment is not fair, and it doesn't always parcel on gender lines or race lines, or anything like that."