The numerical investigation of the radiation emission by a system of two magnetically coupled, long Josephson junctions is reported. Time-dependent synchronized voltage response in the flux-flow regime is analyzed for the case of in-phase and out-of-phase oscillations in the junctions. Simulations show that Josephson junctions operating in the in-phase flux-flow mode may generate rf radiation power by a factor of more than 4 larger than that of a single Josephson junction. The radiation in the out-of-phase flux-flow mode is characterized by nearly completely suppressed amplitudes of odd harmonics and considerably damped even harmonics as compared to that of a single barrier junction. The dependence of the radiation power on the parameter spread between the junctions is investigated. The advantages of using stacked Josephson junctions as oscillators for the sub-mm wave band are discussed.