| Title | Season | Episode # | First Aired |
|---|---|---|---|
| Ishbal Massacre | 2 | 15 | Saturday January 17, 2004 |
| Marcoh's Notes | 2 | 18 | Saturday February 7, 2004 |
| Mom... | 1 | 3 | Saturday October 18, 2003 |
| National Alchemist Qualification Test | 1 | 6 | Saturday November 8, 2003 |
| One is All, All is One | 3 | 28 | Saturday April 17, 2004 |
| Philosopher's Stone | 1 | 8 | Saturday November 22, 2003 |
| Right Hand of Destruction | 2 | 14 | Saturday January 10, 2004 |
| Silver Watch of the Dog of the Military | 1 | 9 | Saturday November 29, 2003 |
| Sin | 3 | 31 | Saturday May 8, 2004 |
| South Headquarters Assault | 3 | 30 | Saturday May 1, 2004 |
| Teacher | 3 | 27 | Saturday April 10, 2004 |
| That Which was Lost | 2 | 16 | Saturday January 24, 2004 |
| The Flame Alchemist/The Fighting Lieutenant/The Mystery of the 13th Warehouse | 3 | 37 | Saturday June 26, 2004 |
| The Genuine Truth Behinds Truths | 2 | 19 | Saturday February 14, 2004 |
| The House Where the Family Waits | 2 | 17 | Saturday January 31, 2004 |
| The Night the Chimera Cries | 1 | 7 | Saturday November 15, 2003 |
| The Reunion of Fools | 3 | 35 | Saturday June 12, 2004 |
| The Scar | 3 | 40 | Saturday July 17, 2004 |
| The Sinner Within Me | 3 | 36 | Saturday June 19, 2004 |
| The Stray Dog Has Run Away | 4 | 43 | Saturday July 31, 2004 |
| The Theory of Greed | 3 | 34 | Saturday June 5, 2004 |
| Thief Siren | 1 | 10 | Saturday December 6, 2003 |
| Those Who Would Challenge the Sun | 1 | 1 | Saturday October 4, 2003 |
| Transmutation of Love | 1 | 4 | Saturday October 25, 2003 |
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