I currently have 3 Fairies that I got from a Great Fairy Fountain. However, I've since opened up two other Great Fairy Fountains and neither of those had fairies around them. I've been playing quite a while and I haven't had them respawn at the first great Fairy Fountain either.
Zelda Breath of the Wild – How to Fix Fairies Not Respawning
zelda-breath-of-the-wild
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Best Answer
Fairies will only respawn if you have less than 3 Fairies.
The number of Fairies that respawn at each Fountain are as follows:
Fairies Left : Fairies at Fountain
3+ : 0
2 : 1
1 : 2
0 : 3
So, release all three fairies and 3 Fairies will spawn at each Fountain, which will allow you to have up to 12 Fairies at once.