- 7 September - Star Trek: New Frontier eBook, The Returned, Part 3, by Peter David.
- 8 September - Titan Books reference book, The Autobiography of James T. Kirk, by David A. Goodman.
- 10 September - IDW Publishing's omnibus edition of Star Trek - Planet of the Apes: The Primate Directive.
- 15 September - The 2016 Star Trek Daily Calendar calendar.
- 17 September - IDW Publishing's Star Trek, Volume 10 trade paperback.
- 29 September -
- Pocket DS9 eBook, The Empty Sack, by Paula M. Block and Terry J. Erdmann.
- "Issue 3" of IDW Publishing's Star Trek - Green Lantern: The Spectrum War.
- "Deity, Part 2", issue 49 of Star Trek: Ongoing.
- Star Trek: New Visions #8, "The Survival Equation" from IDW Publishing.