We present an analysis of kinetics and pulses of zircon growth in migmatites formed at middle to lower crustal depths beneath a volcanic arc. Migmatites in high‐ T metamorphic complexes at active continental margins, such as in the Ryoke Complex of southwest Japan, are thought to have been produced beneath volcanic arcs. Thermal models suggest that melt advection supplies the heat to form such high‐ T complexes. We found that zircons in the migmatites of the Ryoke Complex grew in multiple discrete stages by rapid diffusion‐controlled growth. The individual growth pulses can be distinguished using a Gaussian mixture model when the duration of each growth pulse is shorter than 1σ of the analytical error of the zircon age dating, and where the interval between each growth pulse is larger than 2σ of them. This method allows extraction of the growth pulses even when the zircon exhibits incomplete textural evidence for multiple stages of growth. Application of the method to the Ryoke Complex revealed three and four pulses of zircon growth with 3–10 Myr intervals for two migmatite samples respectively in the Mikawa area and three pulses with 2–4 Myr intervals from one migmatite sample in the Yanai area. The detected zircon growth pulses are consistent with previously reported pulses of plutonic activity in the two areas, with the exception of the oldest growth pulse in the Mikawa area. Therefore, the growth pulses are interpreted to be the result of thermal pulses because of melt flux events at lower to middle crustal levels. The inferred intervals of pulsed melt fluxes are similar to those of individual caldera formation in coeval caldera clusters at the surface.