We study the exchange constants of MnV$_2$O$_4$ using magnetic force theorem and local spin density approximation of density functional theory supplemented with a correction due to on-site Hubbard interaction U. We obtain the exchanges for three different orbital orderings of the Vanadium atoms of the spinel. We then map the exchange constants to a Heisenberg model with single-ion anisotropy and solve for the spin-wave excitations in the non-collinear, low temperature phase of the spinel. The single-ion anisotropy parameters are obtained from an atomic multiplet exact-diagonalization program, taking into effect the crystal-field splitting and the spin-orbit coupling. We find good agreement between the spin waves of one of our orbital ordered setups with previously reported experimental spin waves as determined by neutron scattering. We can therefore determine the correct orbital order from various proposals that exist in the literature.