I find the first unnatural. I would use:
Call him, whether you are going or not. (The instruction is to call him if you are going and call him if you're not. We don't know the reason for the call.)
Alternatively, you could say:
Call him to tell him whether or not you're going. (The instruction is to call him specifically to give him the information about your attendance.)
Tell him by phone whether or not you're going. (Same meaning.)
Your second sentence:
Call him even if you are going. (The instruction ensure the listener knows that they must call him if they are not going but also if they're not going.)