The $O(3)$ non-linear sigma model (NLSM) is a prototypical field theory for QCD and ferromagnetism, and provides a simple system in which to study topological effects. In lattice QCD, the gradient flow has been demonstrated to remove ultraviolet singularities from the topological susceptibility. In contrast, lattice simulations of the NLSM find that the topological susceptibility diverges in the continuum limit, even in the presence of the gradient flow. We introduce a $\theta$-term and analyze the topological charge as a function of $\theta$ under the gradient flow. Our results show that divergence persists in the presence of the flow, even at non-zero $\theta$.