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Looking for filler episodes? View the filler guide.
| # | Title | Aired | Type |
|---|---|---|---|
| 1 | Fullmetal Alchemist | Apr 5, 2009 | Filler |
| 2 | The First Day | Apr 12, 2009 | Canon |
| 3 | City of Heresy | Apr 19, 2009 | Canon |
| 4 | An Alchemist's Anguish | Apr 26, 2009 | Canon |
| 5 | Rain of Sorrows | May 3, 2009 | Canon |
| 6 | Road of Hope | May 10, 2009 | Canon |
| 7 | Hidden Truths | May 17, 2009 | Canon |
| 8 | The Fifth Laboratory | May 24, 2009 | Canon |
| 9 | Created Feelings | May 31, 2009 | Canon |
| 10 | Separate Destinations | Jun 7, 2009 | Canon |
| 11 | Miracle at Rush Valley | Jun 14, 2009 | Canon |
| 12 | One is All, All is One | Jun 21, 2009 | Canon |
| 13 | Beasts of Dublith | Jun 28, 2009 | Canon |
| 14 | Those Who Lurk Underground | Jul 5, 2009 | Canon |
| 15 | Envoy From the East | Jul 12, 2009 | Canon |
| 16 | Footsteps of a Comrade-in-Arms | Jul 19, 2009 | Canon |
| 17 | Cold Flame | Jul 26, 2009 | Canon |
| 18 | The Arrogant Palm of a Small Human | Aug 2, 2009 | Canon |
| 19 | Death of the Undying | Aug 9, 2009 | Canon |
| 20 | Father Before the Grave | Aug 16, 2009 | Canon |
| 21 | Advance of the Fool | Aug 30, 2009 | Canon |
| 22 | Backs in the Distance | Sep 6, 2009 | Canon |
| 23 | Girl on the Battlefield | Sep 13, 2009 | Canon |
| 24 | Inside the Belly | Sep 20, 2009 | Canon |
| 25 | Doorway of Darkness | Sep 27, 2009 | Canon |
| 26 | Reunion | Oct 4, 2009 | Canon |
| 27 | Interlude Party | Oct 11, 2009 | Canon |
| 28 | Father | Oct 18, 2009 | Canon |
| 29 | Struggle of the Fool | Oct 25, 2009 | Canon |
| 30 | The Ishvalan War of Extermination | Nov 1, 2009 | Canon |
| 31 | The 520 Cens Promise | Nov 8, 2009 | Canon |
| 32 | The Fuhrer's Son | Nov 15, 2009 | Canon |
| 33 | The Northern Wall of Briggs | Nov 22, 2009 | Canon |
| 34 | Ice Queen | Nov 29, 2009 | Canon |
| 35 | The Shape of This Country | Dec 6, 2009 | Canon |
| 36 | Family Portrait | Dec 13, 2009 | Canon |
| 37 | The First Homunculus | Dec 20, 2009 | Canon |
| 38 | Conflict at Baschool | Dec 27, 2009 | Canon |
| 39 | Daydream | Jan 10, 2010 | Canon |
| 40 | Homunculus (The Dwarf in the Flask) | Jan 17, 2010 | Canon |
| 41 | The Abyss | Jan 24, 2010 | Canon |
| 42 | Signs of a Counteroffensive | Jan 31, 2010 | Canon |
| 43 | Bite of the Ant | Feb 7, 2010 | Canon |
| 44 | Revving at Full Throttle | Feb 14, 2010 | Canon |
| 45 | The Promised Day | Feb 21, 2010 | Canon |
| 46 | Looming Shadows | Feb 28, 2010 | Canon |
| 47 | Emissary of Darkness | Mar 7, 2010 | Canon |
| 48 | The Oath in the Tunnel | Mar 14, 2010 | Canon |
| 49 | Filial Affection | Mar 21, 2010 | Canon |
| 50 | Upheaval in Central | Mar 28, 2010 | Canon |
| 51 | The Immortal Legion | Apr 4, 2010 | Canon |
| 52 | Combined Strength | Apr 11, 2010 | Canon |
| 53 | Flame of Vengeance | Apr 18, 2010 | Canon |
| 54 | Beyond the Inferno | Apr 25, 2010 | Canon |
| 55 | The Adults' Way of Life | May 2, 2010 | Canon |
| 56 | The Return of the Fuhrer | May 9, 2010 | Canon |
| 57 | Eternal Leave | May 16, 2010 | Canon |
| 58 | Sacrifices | May 23, 2010 | Canon |
| 59 | Lost Light | May 30, 2010 | Canon |
| 60 | Eye of Heaven, Gateway of Earth | Jun 6, 2010 | Canon |
| 61 | He Who Would Swallow God | Jun 13, 2010 | Canon |
| 62 | A Fierce Counterattack | Jun 20, 2010 | Canon |
| 63 | The Other Side of the Gateway | Jun 27, 2010 | Canon |
| 64 | Journey's End | Jul 4, 2010 | Canon |