It means that when someone does something bad to another person, then eventually that same bad thing will happen to him. A lot of people will say it when someone does something bad to them -- indicating that they will take revenge¹.

eg: He felt guilty about what he did, with a feeling that what goes around comes around.

Note:

What goes around comes around的意思是恶有恶报。如果你对别人不好，最终不好的事情也会发生在你身上。当受到伤害时，很多人会说这句话来诅咒。

例：他为他的所做所为感到心虚，害怕遭到报应