We present a Raman study of Fe3O4 (100) thin films across the Verwey transition in the temperature range of 85–300K. These films are epitaxially grown on MgO (100) substrate by pulsed laser deposition technique. X-ray diffraction and low temperature resistivity measurements reveal that these films exhibit high structural order and perfect stoichiometry with Verwey transition at 121K. The frequency of different Raman modes [A1g and T2g(2)] changes abruptly around the Verwey transition temperature (TV). Below TV we observe a splitting in T2g(3) mode. Using Allen’s formula [Solid State Commun. 14, 937 (1974)] the strength of the electron-phonon coupling (λ) is estimated from the observed line shape parameters, and our estimates show that in epitaxially grown Fe3O4 thin films strong electron-phonon coupling is present. This coupling parameter is larger for T2g(3) mode as compared with that of A1g and T2g(2) modes. It is also observed that the coupling parameter corresponding to A1g mode remains invariant going from bulk single crystal to thin film while that of T2g(2) and T2g(3) modes are almost doubled. An attempt has been made to correlate the observed behavior with the presence of antiphase boundary in epitaxial thin films.