Nick here from Shopify. Good question!
Pre-Paid Credit Cards will work in some cases but not all. In most cases, Shopify typically doesn't accept Pre-Paid Credit Cards as many of these cards have unusual policies as they are not your regular type of credit card. However, in some instances we will be able to accept pre-paid credit cards, however, in these instances, you would need to work with the associated network and or bank to allow recurring payment charge types. I understand it's not as simple to get credit cards in some places around the world, but it is always recommended to pay via credit card whenever possible for your Shopify plan. So to answer your question, it's possible but not guaranteed.
Accepting payments from customers with prepaid credit cards should not be a problem at all once you have your payment gateway set up. It might be worth reaching out to your payment gateway to double-check but I would lean to it being ok.
Hope this helps and answers your question.
All the best, Nick