I'm trying to use Green's theorem to calculate the flux of $F$ through some curve. However, is it possible to use Green's theorem if the divergence of $F$ is $0$?

I'm trying to use Green's theorem to calculate the flux of $F$ through some curve. However, is it possible to use Green's theorem if the divergence of $F$ is $0$?

Of course. That means you're integrating $0$ over some area, the result of that is $0$, so the flux through the curve is $0$. Be careful that the divergence is defined at each point inside the curve.