You need to wait at least 48 hours after it rains before you stain your deck.
Before staining your deck after it rains you need to wait long enough to allow the wood deck to dry out fully so that the stain will be absorbed properly into the wood.
When the wood deck is too wet the wood will have absorbed the water and then there won't be any room for the decks wood to absorb the stain.
So you need to wait at least 48 hours after it rains on the deck to apply the stain to your deck.
Sometimes the deck may be dry enough within 24 hours but I would recommend waiting at least 48 hours to allow enough time for the deck to dry out enough from the rain.
Then the deck stain will absorb much better into the wood deck.