We develop an analytic theory for the recently demonstrated Josephson Junction laser (Science 355, p. 939, 2017). By working in the time-domain representation (rather than the frequency-domain) a single non-linear equation is obtained for the dynamics of the device, which is fully solvable in some regimes of operation. The nonlinear drive is seen to lead to mode-locked output, with a period set by the round-trip time of the resonant cavity.