Here is a list of Pokémon Y's version exclusive Pokémon. Just like previous Pokémon games, Pokémon X and Pokémon Y have version specific Pokémon that can only be found and caught in the version they are specific to.
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| Pokémon | Ability | Type | Appearance |
| Yveltal | Dark Aura | Dark/Flying | |
| Mega Charizard Y | Drought | Fire/Flying | |
| Shellder | Shell Armor, Skill Link | Water | |
| Cloyster | Shell Armor, Skill Link | Water | |
| Mega Mewtwo Y | Insomnia | Psychic | |
| Heracross | Guts, Swarm | Bug/Fighting | |
| Larvitar | Guts | Rock/Dark | |
| Pupitar | Shed Skin | Rock/Dark | |
| Tyranitar | Sand Stream | Rock/Dark | |
| Electrike | Static, Lightning Rod | Electric | |
| Manectric | Static, Lightning | Electric | |
| Throh | Guts, Inner Focus | Fight | |
| Spritzee | Aroma Veil | Fairy | |
| Aromatisse | Healer | Fairy | |
| Purrloin | Limber, Unburden | Dark | |
| Liepard | Limber, Unburden | Dark | |
| Skrelp | Poison Point, Poison Touch | Poison/Water | |
| Dragalge | Poison Point, Poison Touch | Poison/Dragon |