Objective To examine the relationship between stigma experience related to facial appearance in Japanese youths with cleft lip and/or palate (CL/P) and their self-perception. Design A cross-sectional study. Participants Sixty-nine Japanese youths with CL/P (11-18 years old) Outcome measures The participants’ stigma experience in relation to facial appearance (measured with 7 single contextual scale items) and their self-perception (measured with 5 domain scores based on 30 perceptual items) were assessed using the Japanese version of the Youth Quality of Life Instrument-Facial Differences Module. Participants were categorized into high and low self-perception subgroups with a threshold of 1 standard deviation for each domain. The frequency of stigma experiences was compared between the following 2 subgroups: age, sex, cleft palate only versus other cleft, and high versus low self-perception. Correlations between the responses regarding stigma and all domain scores were examined. Results Sixteen percent of the participants reported experiencing stigma. Hearing others say something about their face occurred significantly more frequently in youths 15 to 18 years of age than in youths 11 to 14 years of age. Stigma frequency was not found to differ by sex or cleft type. Stigma experiences were significantly more frequent for youth with higher scores across negative self-perception domains as well as higher coping skills. Significant correlations were identified between responses regarding stigma items and all domain scores ( r  =  0.27-0.63, p < .05). Conclusions It was found that stigma experiences related to facial appearance may influence negative self-perceptions of facial differences as well as higher coping skills among Japanese youths with CL/P.