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.