In this paper, we strengthen a result by Green about an analogue of Sarkozy's theorem in the setting of polynomial rings $\mathbb{F}_q[x]$. In the integer setting, for a given polynomial $F \in \mathbb{Z}[x]$ with constant term zero, (a generalization of) Sarkozy's theorem gives an upper bound on the maximum size of a subset $A \subset \{1, \ldots, n \}$ that does not contain distinct $a_1,a_2 \in A$ satisfying $a_1 - a_2 = F(b)$ for some $ b \in \mathbb{Z}$. Green proved an analogous result with much stronger bounds in the setting of subsets $A \subset \mathbb{F}_q[x]$ of the polynomial ring $\mathbb{F}_q[x]$, but required the additional condition that the number of roots of the polynomial $F \in \mathbb{F}_q[x]$ is coprime to $q$. We generalize Green's result, removing this condition. As an application, we also obtain a version of Sarkozy's theorem with similarly strong bounds for subsets $A \subset \mathbb{F}_q$ for $q = p^n$ for a fixed prime $p$ and large $n$.