It depends on the characteristics of the case and how far it stands the phone off from the base. For what it's worth, my last phone with Qi was a Blackberry Pr

It depends on the characteristics of the case and how far it stands the phone off from the base. For what it's worth, my last phone with Qi was a Blackberry Priv with an Otterbox Defender case, and it charged just fine. I'd be very surprised if Apple didn't make allowances for something that common.