The development of live organisms is precisely regulated by a sequence of gene functions even in the presence of biological noises. However, it is difficult to evaluate the effect of the noises in vivo and the mechanisms how the noise is filtered during development is largely unknown. To unveil the noise canceling mechanism, we use the fly visual system, where the timing of differentiation of neural stem cells is spatio-temporally ordered. Our mathematical modeling predicts that JAK/STAT signaling plays a role in noise canceling to guarantee the robust progression of the differentiation wave in silico. We further demonstrate that the suppression of JAK/STAT signaling causes stochastic and ectopic neural stem cell differentiation in vivo, suggesting an evolutionally conserved function of JAK/STAT to regulate the robustness of stem cell differentiation.