We report an inelastic x-ray scattering investigation of phonons in FeSe superconductor. Comparing the experimental phonon dispersion with density functional theory (DFT) calculations in the non-magnetic state, we found a significant disagreement between them. Improved overall agreement was obtained by allowing for spin-polarization in the DFT calculations, despite the absence of magnetic order in the experiment. This calculation gives a realistic approximation, at DFT level, of the disordered paramagnetic state of FeSe, in which strong spin fluctuations are present.