Self-concept develops during adolescence, but little is known about self-concept in adolescents with autism. This behavioral neuroimaging study investigated (1) self-concept positivity across three domains (academic, physical appearance, and prosocial) and (2) from the perspective of self (direct self-concept) and the perceived perspective of peers (reflected self-concept) in 12- to 16-year-old adolescent males with (n = 35) and without autism (n = 34). These behavioral and neural measures of self-concept were additionally related to autism traits and alexithymia traits across groups. Results showed no general group differences, but more autism traits were related to less positive self-concept ratings in the physical appearance and prosocial domains. More autism traits were also associated with less similarity between direct and reflected prosocial self-concept ratings. Lower self-esteem was additionally explained by alexithymia, specifically the difficulty to identify ones feelings. Participants showed medial prefrontal cortex activation in response to evaluating self-traits in both groups. Region-of-interest analyses revealed that medial prefrontal cortex and right temporal-parietal junction activation were differentially related to alexithymia traits. Together, this study provides a comprehensive understanding of self-concept and self-esteem in adolescents with varying levels autism and alexithymia traits.