Subgraph counting is a fundamental and well-studied problem whose computational complexity is well understood. Quite surprisingly, the hypergraph version of subgraph counting has been almost ignored. In this work, we address this gap by investigating the most basic sub-hypergraph counting problem: given a (small) hypergraph $H$ and a (large) hypergraph $G$, compute the number of sub-hypergraphs of $G$ isomorphic to $H$. Formally, for a family $\mathcal{H}$ of hypergraphs, let #Sub($\mathcal{H}$) be the restriction of the problem to $H \in \mathcal{H}$; the induced variant #IndSub($\mathcal{H}$) is defined analogously. Our main contribution is a complete classification of the complexity of these problems. Assuming the Exponential Time Hypothesis, we prove that #Sub($\mathcal{H}$) is fixed-parameter tractable if and only if $\mathcal{H}$ has bounded fractional co-independent edge-cover number, a novel graph parameter we introduce. Moreover, #IndSub($\mathcal{H}$) is fixed-parameter tractable if and only if $\mathcal{H}$ has bounded fractional edge-cover number. Both results subsume pre-existing results for graphs as special cases. We also show that the fixed-parameter tractable cases of #Sub($\mathcal{H}$) and #IndSub($\mathcal{H}$) are unlikely to be in polynomial time, unless respectively #P = P and Graph Isomorphism $\in$ P. This shows a separation with the special case of graphs, where the fixed-parameter tractable cases are known to actually be in polynomial time.