The Calfornication star and Leoni are said to have decided to take time apart in order to decide whether or not to proceed with their marriage, reports TMZ.
The couple separated briefly in 2008 after Duchovny's admission that he suffered from sex addition and he voluntarily entered rehab for the affliction.
Duchovny later claimed that he had never felt better after completing treatment and reuniting with Leoni.
He and Leoni married in 1997 and are parents to 12-year-old Madelaine West and 9-year-old Kyd Miller.
Leoni's new pilot Spring/Fall - which focuses on the fashion world in New York City was recently picked up by HBO.
Duchovny's Californication will return for a fifth season on Showtime later this year and will jump three years from its season four finale.
Both Leoni and Duchovny were invited to join the Academy of Motion Picture Arts and Sciences earlier this month.