In this trial, nasopharyngeal cancer stem cells (CSCs) were separated and cultured to produce a vaccine; its safety and efficacy were prospectively evaluated in low-, medium-, and high-dose groups. Between April and September 2014, we enrolled 90 patients who met the enrolment criteria, and assigned them to three groups (n=30). Throughout the trial, injection site reaction was the most common reaction (81%), and fever was least common (31%); however, there was no difference among the three groups. When the immune responses pre- and post-vaccination were compared, we found that the CSC-specific and -nonspecific response in the medium- and high-dose groups were both significantly enhanced. This study is the first clinical trial of a nasopharyngeal CSC vaccine and preliminarily proves its safety and efficacy. Keywords:Cancer prevention; Cancer stem cell; Efficacy; Immunotherapy; Nasopharyngeal cancer; Safety; Vaccine.