 
     
        Season 4 is the season where the maturity of The X-Files truly shines. The production budget has grown larger, and in accordance, the visual effects of The X-Files have reached a level surpassing that of many movies. With Darin Morgan gone, comedy writer Vince Gilligan stepped in, and Gilligan's work brought light and witty humor to The X-Files.
| Name | First Aired | Runtime | Image | |
|---|---|---|---|---|
| S04E01 | Herrenvolk (2) | October 4, 1996 FOX | 45 | |
| S04E02 | Home | October 11, 1996 FOX | 45 | |
| S04E03 | Teliko | October 18, 1996 FOX | 45 | |
| S04E04 | Unruhe | October 27, 1996 FOX | 45 | |
| S04E05 | The Field Where I Died | November 3, 1996 FOX | 45 | |
| S04E06 | Sanguinarium | November 10, 1996 FOX | 45 | |
| S04E07 | Musings of a Cigarette Smoking Man | November 17, 1996 FOX | 45 | |
| S04E08 | Tunguska (1) | November 24, 1996 FOX | 45 | |
| S04E09 | Terma (2) | December 1, 1996 FOX | 45 | |
| S04E10 | Paper Hearts | December 15, 1996 FOX | 45 | |
| S04E11 | El Mundo Gira | January 12, 1997 FOX | 45 | |
| S04E12 | Leonard Betts | January 26, 1997 FOX | 45 | |
| S04E13 | Never Again | February 2, 1997 FOX | 45 | |
| S04E14 | Memento Mori | February 9, 1997 FOX | 45 | |
| S04E15 | Kaddish | February 16, 1997 FOX | 45 | |
| S04E16 | Unrequited | February 23, 1997 FOX | 45 | |
| S04E17 | Tempus Fugit (1) | March 16, 1997 FOX | 45 | |
| S04E18 | Max (2) | March 23, 1997 FOX | 45 | |
| S04E19 | Synchrony | April 6, 1997 FOX | 45 | |
| S04E20 | Small Potatoes | April 20, 1997 FOX | 45 | |
| S04E21 | Zero-Sum | April 27, 1997 FOX | 45 | |
| S04E22 | Elegy | May 4, 1997 FOX | 45 | |
| S04E23 | Demons | May 11, 1997 FOX | 45 | |
| S04E24 | Gethsemane (1) season finale | May 18, 1997 FOX | 45 |