We consider the Stokes system in a thin porous medium Ωε of thickness ε which is perforated by periodically distributed solid cylinders of size ε. On the boundary of the cylinders we prescribe non-homogeneous Fourier boundary condition depending on a parameter γ. The aim is to give the asymptotic behavior of the velocity and the pressure of the fluid as ε goes to zero. Using an adaptation of the unfolding method, we give, following the values of γ, different limit systems.