A Čech complex of a finite simple graph $G$ is a nerve complex of balls in the graph, with one ball centered at each vertex. More precisely, let the Čech complex $\mathcal{N}(G,r)$ be the nerve of all closed balls of radius $\frac{r}{2}$ centered at vertices of $G$, where these balls are drawn in the geometric realization of the graph $G$ (equipped with the shortest path metric). The simplicial complex $\mathcal{N}(G,r)$ is equal to the graph $G$ when $r=1$, and homotopy equivalent to the graph $G$ when $r$ is smaller than half the length of the shortest loop in $G$. For higher values of $r$, the topology of $\mathcal{N}(G,r)$ is not well-understood. We consider the $n$-dimensional hypercube graphs $\mathbb{I}_n$ with $2^n$ vertices. Our main results are as follows. First, when $r=2$, we show that the Čech complex $\mathcal{N}(\mathbb{I}_n,2)$ is homotopy equivalent to a wedge of 2-spheres for all $n\ge 1$, and we count the number of 2-spheres appearing in this wedge sum. Second, when $r=3$, we show that $\mathcal{N}(\mathbb{I}_n,3)$ is homotopy equivalent to a simplicial complex of dimension at most 4, and that for $n\ge 4$ the reduced homology of $\mathcal{N}(\mathbb{I}_n, 3)$ is nonzero in dimensions 3 and 4, and zero in all other dimensions. Finally, we show that for all $n\ge 1$ and $r\ge 0$, the inclusion $\mathcal{N}(\mathbb{I}_n, r)\hookrightarrow \mathcal{N}(\mathbb{I}_n, r+2)$ is null-homotopic, providing a bound on the length of bars in the persistent homology of Čech complexes of hypercube graphs.