We report on the observation of the spin Seebeck effect in antiferromagnetic MnF$_2$. A device scale on-chip heater is deposited on a bilayer of Pt (4 nm)/MnF$_2$ (110) (30 nm) grown by molecular beam epitaxy on a MgF$_2$ (110) substrate. Using Pt as a spin detector layer it is possible to measure thermally generated spin current from MnF$_2$ through the inverse spin Hall effect. The low temperature (2 - 80 K) and high magnetic field (up to 140 kOe) regime is explored. A clear spin flop transition corresponding to the sudden rotation of antiferromagnetic spins out of the easy axis is observed in the spin Seebeck signal when large magnetic fields (>9 T) are applied parallel the easy axis of the MnF$_2$ thin film. When magnetic field is applied perpendicular to the easy axis, the spin flop transition is absent, as expected.