Episode Premieres
- January 1, 12:01am - Gamera vs Zigra - First appearance of Dr. Forrester and Dr. Erhardt; Remade in Season 3 - See Gamera vs Zigra NOTE: Most sources list the airdate as December 31, 1988, but since it aired at midnight, it was actually the first episode of 1989.
- January 8 - Gamera vs Guiron - Remade in Season 3 - See Gamera vs Guiron
- January 15 - Phase IV
- January 22 - Cosmic Princess
- January 29 - Humanoid Woman
- February 5 - Fugitive Alien - Remade in Season 3 - See Fugitive Alien
- February 19 - MST3K K13 - SST- Death Flight
- March 5 - Mighty Jack- Remade in Season 3 - See Mighty Jack
- March 12 - Superdome
- March 19 - City on Fire
- April 2 - Time of the Apes - Remade in Season 3 - See Time of the Apes
- May 7 - The Million Eyes of Sumuru
- May 14 - Hangar 18
- May 21 - The Last Chase
- May 28 - The Legend of the Dinosaurs - Final KTMA episode
- November 18 - The Robot vs the Aztec Mummy - First episode to air on Comedy Channel, first Season 1 episode to air, Joel Hodgson's first appearance as Joel Robinson, Jim Mallon's first appearance as Gypsy, first short shown, earliest episode to be released on DVD.
- November - The Crawling Eye - First episode produced for Season 1.
- December - The Mad Monster
- December - The Corpse Vanishes
- December - The Crawling Hand
- December - Robot Monster
- December - The Slime People