To support children with chronic diseases, reference values to measure developmental changes in self-perception and self-esteem are considered a useful yardstick. To develop reference values to measure self-perceived competence and self-esteem in Japanese children, the Children’s Perceived Competence Scale (CPCS) was administered to 768 children of elementary school grade 1 (6 years) to grade 6 (11 years) at four public schools in Japan, from November to December 2012. After excluding 74 with chronic diseases and/or incomplete responses, 694 children were included. CPCS measures children’s self-perceived competence in cognitive, social, physical domains, and general self-worth, namely self-esteem. There was a tendency for scores of cognitive and general self-worth to decrease with increasing grade. Scores among grade 5 respondents were significantly lower than those among grade 4 respondents for both social and physical domains. Scores among boys and girls differed significantly, with boys scoring higher for physical domain in grades 3 and 6 and for general self-worth domain in grade 6. The CPCS reference values to measure self-perceived competence and self-esteem in Japanese children were developed in this study. These reference values are useful to inform practitioners supporting children with psychological or psychiatric problems or those with chronic diseases.