Individuals with neurodevelopmental disorders (NDDs) are more susceptible to developing severe or resistant mood disorders. However, they often face challenges in accessing specific treatments. To understand the barriers to treatment in this group, we conducted a secondary analysis of a multicenter observational study on 305 adolescents referred to specialized care (mean age 14.38 ± 0.13 years, 57% girls, 9% bipolar disorder, 91% depressive disorders). NDDs were categorized based on the number of co-occurring NDDs for each subject (none: 67%, one: 18%, two: 7%, three: 5%, four and more: 2%). We explored the predictive value of the number of NDDs on various clinical and therapeutic factors. The analysis revealed significant associations between the number of NDDs and the duration of mood symptoms, persistent irritability, associated disruptive behavioral disorders, lower scores on the Children’s Global Assessment Scale (CGAS) at baseline, and polypharmacy. The number of NDDs did not correlate with the use of antidepressants, the Clinical Global Impression-Improvement scale (CGI-I) at discharge, or changes in the CGAS score during the stay. The challenges in distinguishing mood disorders from chronic emotional and behavioral difficulties may contribute to the difficulties in accessing specific care for mood disorders. These results suggest that treatments for mood disorders demonstrate comparable effectiveness when provided regardless of the associations with NDDs.