It really does depend on the context/situation.
If someone has done you a favour and you tell them that you don't know how to thank them, they could say: "You can thank me later" in the sense of that you can do them a favour later and help them with something.

If someone does you a favour and you don't thank them for it and don't seem grateful, they may say in a joking or sarcastic way: "You can thank me later" as a gentle or subtle (even unsubtle) reminder that you should be grateful to them.

If someone gives you a word of warning or tips to avoid you getting into a crisis and you think the advice is unnecessary, they might say: "You can thank me later" or "you'll thank me later" in the sense that although you don't take their words/actions seriously now you'll eventually realise that they were right and will be grateful to them - even if you're not grateful now.
by tarik99 February 25, 2017
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