Morris and Saxton used the method of containers to bound the number of $n$-vertex graphs with $m$ edges containing no $\ell$-cycles, and hence graphs of girth more than $\ell$. We consider a generalization to $r$-uniform hypergraphs. The {\em girth} of a hypergraph $H$ is the minimum $\ell$ such that for some $F \subseteq H$, there exists a bijection $φ: E(C_\ell) \to E(F)$ with $e\subseteq φ(e)$ for all $e\in E(C_\ell)$. Letting $N_m^r(n,\ell)$ denote the number of $n$-vertex $r$-uniform hypergraphs with $m$ edges and girth larger than $\ell$ and defining $λ= \lceil (r - 2)/(\ell - 2)\rfloor$, we show \[ N_m^r(n,\ell) \leq N_m^2(n,\ell)^{r - 1 + λ}\] which is tight when $\ell - 2 $ divides $r - 2$ up to a $1 + o(1)$ term in the exponent. This result is used to address the extremal problem for subgraphs of girth more than $\ell$ in random $r$-uniform hypergraphs.