Magento – Currency switcher not working for currency AED in Magento 2

According to the Magento Knowledge Base:

1. In the Base Currency list, select the primary currency that is used for store transactions.
2. In the Default Display Currency list, select the primary currency that is used to display pricing in your store.
3. In the Allowed Currencies list, select all currencies that are accepted as payment by your store.

I will paraphrase the answer of St0iK. You can't set different base currency per store, but you can do it per website. First you have to go to the admin panel -> System -> Configuration -> CATALOG -> Catalog -> Price -> Catalog Price Scope and change it from Global to Website. Now when you go to the admin panel -> System -> Configuration -> GENERAL -> Currency Setup -> Currency Options you can change Base Currency per Website, not only for Default (Global). So you have to transfer you stores to websites and you will be able to do what you want.