The arithmetic regularity lemma for $Fpn$, proved by Green in 2005, states that given a subset $A\subseteq Fpn$, there exists a subspace $H\le Fpn$ of bounded codimension such that $A$ is Fourier-uniform with respect to almost all cosets of $H$. It is known that in general, the growth of the codimension of $H$ is required to be of tower type depending on the degree of uniformity, and that one must allow for a small number of non-uniform cosets. Our main result is that, under a natural model-theoretic assumption of stability, the tower-type bound and non-uniform cosets in the arithmetic regularity lemma are not necessary. Specifically, we prove an arithmetic regularity lemma for $k$-stable subsets $A\subseteq Fpn$ in which the bound on the codimension of the subspace is a polynomial (depending on $k$) in the degree of uniformity, and in which there are no non-uniform cosets. This result is an arithmetic analogue of the stable graph regularity lemma proved by Malliaris and Shelah.