Phonons are the main source of relaxation in molecular nanomagnets, and different mechanisms have been proposed in order to explain the wealth of experimental findings. However, very limited experimental investigations on phonons in these systems have been performed so far, yielding no information about their dispersions. Here we exploit state-of-the-art single-crystal inelastic neutron scattering to directly measure for the first time phonon dispersions in a prototypical molecular qubit. Both acoustic and optical branches are detected in crystals of [VO(acac)[Formula: see text]] along different directions in the reciprocal space. Using energies and polarisation vectors calculated with state-of-the-art Density Functional Theory, we reproduce important qualitative features of [VO(acac)[Formula: see text]] phonon modes, such as the presence of low-lying optical branches. Moreover, we evidence phonon anti-crossings involving acoustic and optical branches, yielding significant transfers of the spin-phonon coupling strength between the different modes.