| Episode | air date | star date |
| The Man Trap CharlieX Where No Man Has Gone Before The Naked Time | 9/8/66 | 1513.1 |
| 9/15/66 | 1533.6 | |
| 9/2/66 | 1312.4 | |
| 9/29/66 | 1704.2 | |
| The Enemy Within Mudd's Women What Are Little Girls Made Of? Miri | 10/6/66 | 1672.1 |
| 10/13/66 | 1329.8 | |
| 10/20/66 | 2712.4 | |
| 10/27/66 | 2713.5 | |
| Dagger of the Mind The Corbomite Maneuver The Menagerie, Part I Part II The Conscience of the King | 11/3/66 | 2715.1 |
| 11/10/66 | 1512.2 | |
| 11/17/66 | 3012.4 | |
| 11/24/66 | 3013.1 | |
| 12/8/66 | 2817.6 | |
| Balance of Terror Shore Leave The Galileo Seven The Squire of Gothos | 12/15/66 | 1709.2 |
| 12/29/66 | 3025.3 | |
| 1/5/67 | 2821.5 | |
| 1/12/67 | 2124.5 | |
| Arena Tomorrow Is Yesterday Court Martial The Return of the Archons | 1/19/67 | 3045.6 |
| 1/26/67 | 3113.2 | |
| 2/2/67 | 2947.3 | |
| 2/9/67 | 3156.2 | |
| Space Seed A Taste of Armageddon This Side of Paradise The Devil in the Dark | 2/16/67 | 3141.9 |
| 2/23/67 | 3192.1 | |
| 3/2/67 | 3417.3 | |
| 3/9/67 | 3196.1 | |
| Errand of Mercy The Alternative Factor The City on the Edge of Forever Operation: Annihilate! | 3/23/67 | 3198.4 |
| 3/30/67 | 3087.6 | |
| 4/6/67 | 3134.0 | |
| 4/13/67 | 3287.2 |