Transgender children and adolescents show high rates of co-occurring psychopathology, which might be related to low self-confidence. Earlier research showed that compared to the norm population, transgender clinic–referred children have lower self-perception on two domains: physical appearance and global self-worth. This study aimed to compare self-perception in a sample of transgender clinic–referred children and adolescents with their standardization samples and to examine differences between these two groups. To measure self-esteem, the Self-Perception Profile for Children was administered to 305 referred children (162 assigned males at birth (AMABs) and 143 assigned females at birth (AFABs), mean age = 9.05 (SD, 1.47), range = 5.9–13.00 years), and the Self-Perception Profile for Adolescents was administered to 369 referred adolescents (118 AMABs and 251 AFABs, mean age = 15.27 (SD, 1.80), range = 10.73–18.03 years). To measure the severity of gender dysphoria, the parents of the children completed the Gender Identity Questionnaire and the adolescents completed the Utrecht Gender Dysphoria Scale. Referred children and adolescents had a significantly lower self-concept compared to the normative population, whereby referred adolescents felt less competent compared to referred children. Compared to their peers, childhood referred AFABs perceived themselves even better on scholastic and athletic competence and social acceptance. With regard to gender differences, referred AFABs generally showed a better self-perception compared to referred AMABs. The lower self-perception of transgender clinic–referred children and adolescents compared to same age peers deserves clinical attention and interventions aimed at, for example, improving social and physical self-worth.