Abstract Under specific conditions, cultured human embryonic stem cells (hESCs) corresponding to primed post-implantation epiblasts can be converted back to a ‘naïve pluripotency’ state that resembles the pre-implantation epiblasts. The core pluripotency factor OCT4 is known to be crucial in regulating different states of pluripotency, but its potential regulatory role in human naïve pluripotency remains unexplored. In this study, we systematically mapped out phosphorylation sites in OCT4 protein that are differentially phosphorylated between two states of pluripotency, and further identified ATR as a key kinase that phosphorylated OCT4 in naïve but not primed hESCs. The kinase activity levels of ATR in naïve hESCs were higher than those in primed hESCs. Ablating cellular ATR activity significantly halted the induction of naïve hESCs from their primed counterparts, and increased early apoptotic death of naïve hESCs upon UV and CPT treatment. Thus, our work reveals the importance of ATR activity in safeguarding human naïve pluripotency, and implicates a potential association of OCT4 phosphorylation, DNA damage sensing and repairing system in regulating different states of pluripotency during early development.