Though the revival was announced a few months ago, Duchovny admits it had been in the pipeline for "a couple of years" but has taken until now for schedules to allow it to happen.
He told Vulture: We start shooting in June. It's something that we've been working on behind the scenes for quite a while.
"It took a lot of planning to get the three of us - [creator] Chris Carter, Gillian, and I - to be able to commit to being in the same place at the same time for as long as it's going to take to do the show.
"This is something we've all been talking about for a couple of years."
The cult sci-fi series originally ran from 1993 to 2002 and Gillian has previously admitted she and David didn't always get on well when they were filming the show.
She recently said: "There were definitely periods when we hated each other ... hate is too strong a word.
"We didn't talk for long periods of time. It was intense, and we were both pains in the ass for the other at various times."
But the pair did reprise their roles as Mulder and Scully in 2008 movie The X-Files: I Want to Believe, which was written and directed by Chris and also starred Amanda Peet and Billy Connolly.
Duchovny on new record; emotional reading X-Files script
Whether you remember him as FBI agent Mulder from The X-Files or the womanizing novelist Hank Moody on Californication, David Duchovny wants you to know him as something else: The 54-year old actor recently released his first album, Hell or Highwater.
The actor-director claims he's never set out to do pursue a career in music. He credits his children for sending him in a new direction.
"I'm always telling them to try new things, but that's BS because I don't try new things," he said.
So he took his own advice: He learned to play guitar and began writing and playing his own songs.
Recently, Duchovny sat down to talk about the record, which was released this week, and The X Files sequel which Fox will roll out in January.
Revisiting X-Files, what's it like getting back into that?
Duchovny: I actually just got the first script and found it was a very oddly emotional moment. I scrolled down on the script I saw the name Mulder and dialogue underneath it; I actually started to tear up. I didn't expect that at all.
Tell me about the fandom of playing Mulder?
In this decade I've done a lot of other work and I feel like that will always be the most popular thing I'll ever do ... so that's OK with me. I realize that there's something that comes with that: you'll always be that guy in some way. But personally, I no longer have any anxiety about being typecast or being remembered that way because I feel fulfilled in stuff that I've done.
What gave you the courage to do an album?
I feel like I reached an age in my life where I don't necessarily want to listen to the nay sayers. I learned how to play guitar four or five years ago by myself. The project then was to just play guitar enough so that I could amuse myself alone... Then I just thought why can't I come up with a melody, or two, or 12.
Who inspired you to record?
Duchovny: The actual inspiration of the whole thing was really my kids. ... I tell them about skills, about life skills about anything you're going to do. So I thought, well what about the guitar. I'll learn how to play the guitar in front of them. They can watch me struggle and be very poor at something and keep going.
- Bang! Showbiz with AP