Size is the difference. That is, the size of the indentations. Both are usually made of a non-stick metal but the holes in which you pour the batter are larger and more shallow in a whoopie pie pan than its muffin counterpart. They are also typically shaped like a half-moon or an oval, rather than a circle. As well, a muffin pan bakes individual muffins, whereas the whoopie pie pan bakes two halves that are then united along with the cream to form one delicious treat.