Skeletal muscle stem cells (also called satellite cells, SCs) are important for maintaining muscle tissue homeostasis and damage-induced regeneration. However, it remains poorly understood how the SC quiescence is preserved. Here we report that AP-1 family member ATF3 preserves the SC quiescence by preventing their premature activation. Atf3 is rapidly and transiently induced in SCs upon activation. Short-term deletion of Atf3 in SCs accelerates acute injury-induced regeneration, and however, its long-term deletion exhausts the SC pool and thus impairs muscle regeneration. The Atf3 loss also provokes SC activation during voluntary exercise and enhances SC activation during resistance exercise. Mechanistically, ATF3 directly activates the transcription of Histone 2B genes, which reduction accelerates nucleosome displacement and gene transcription required for SC activation. Finally, the ATF3-dependent H2B expression also prevents genome instability and replicative senescence in SCs. Therefore, this study has revealed a novel mechanism for preserving the SC population by actively suppressing precocious activation, in which ATF3 is a key regulator.