Background: Co-occurring conditions and psychiatric comorbidities are more frequently observed in autistic individuals than in typically developing populations. Objective: The present study aimed to investigate the agreement of parent- and self-reported psychopathological assessment using the Child Behavior Checklist (CBCL/6-18) and the Youth Self Report (YSR/11-18), respectively, in autistic adolescents without intellectual impairment. Methods: 54 autistic adolescents without intellectual impairment (11–18 years; M = 14.73; SD = 2.28) were assessed with a psychiatric and psychological evaluation conducted by expert clinicians also using self- and parent-reported scales and semi-structured interviews (K-SADS PL, CDI, MASC) including CBCL/6-18 and YSR/11-18. Results: According to clinical judgment, over 90% of participants had at least a comorbidity: anxiety (68.5%) and mood disorder (57.4%) were the most frequent. The results indicate significant discrepancies between parent- and self-reports across the three summary scales, which assess emotional and behavioral problems, as well as their combined presentation, often observed in youth with ASD. Specifically, differences were found in Internalizing (p < 0.001), Externalizing (p = 0.013), and Total Problems (p < 0.001) scales. Conclusions: The findings show the lack of agreement in parent- and self-reported scales in our sample. These results suggest the need for a cross- and multi-informant approach to support clinical judgment and understand psychopathological comorbidities of autistic adolescents without intellectual impairment.