Pluripotent stem cells have great potential for developmental biology and regenerative medicine. Embryonic stem cells, which are obtained from blastocysts, and induced pluripotent stem cells, which are generated by the reprogramming of somatic cells, are two main types of pluripotent cells. It is important to understand the regulatory network that controls the pluripotency state and reprogramming process. Various types of noncoding RNAs (ncRNAs) have emerged as substantial components of regulatory networks. The most studied class of ncRNAs in the context of pluripotency and reprogramming is microRNAs (miRNAs). In addition to canonical microRNAs, other types of small RNAs with miRNA-like function are expressed in PSCs. Another class of ncRNAs, long ncRNAs, are also involved in pluripotency and reprogramming regulation. Thousands of ncRNAs have been annotated to date, and a significant number of the molecules do not have known function. In this review, we briefly summarized recent advances in this field and described existing genome-editing approaches to study ncRNA functions.