The first series was published by Topps Comics and ran for 41 issues from January 1995 to September 1998, coinciding with the second through fifth seasons of the television program.

In 1996, Topps published X-Files #0, an adaptation of the pilot episode, in order to test the market for a series adapting the episodes of the X-Files TV series. The issue was successful, and X-Files Season One ran for nine issues (August 1997–July 1998). The series's name was provisional, and Topps in fact intended to adapt every episode, but never got as far as season two. The series was written by Roy Thomas, who would create a first draft for each issue by working off of the episode's script, then watch the actual episode and modify his work to account for changes made on the set.