Objectives: The purpose of this study was to assess differences in the outcomes of youth with schizophrenia-spectrum disorders (SCZ-S) and psychotic disorder not otherwise specified (PsyNOS) during early antipsychotic treatment. Methods: The study was a prospective, naturalistic, inception cohort study of youth £ 19 years old with SCZ-S (schizophrenia, schizoaffective disorder, schizophreniform disorder) or PsyNOS (PsyNOS, brief psychotic disorder) and £ 24 months of lifetime antipsychotic treatment receiving clinician's choice antipsychotic treatment. Baseline demographic, illness and treatment variables, and effectiveness outcomes were compared at 12 weeks last-observation-carried-forward across SCZ-S and PsyNOS patients, adjusting for significantly different baseline variables. Results: Altogether, 130 youth with SCZ-S (n = 42) or PsyNOS (n = 88), mostly antipsychotic naïve (76.9%), were prescribed risperidone (47.7%), olanzapine (19.2%), aripiprazole (14.6%), quetiapine (11.5%), or ziprasidone (6.9%). Compared with those with PsyNOS, SCZ-S youth were older (16.4 -2.1 vs. 14.8 -3.2, p = 0.0040), and less likely to be Caucasian (19.1% vs. 42.5%, p = 0.009). At baseline, SCZ-S patients had significantly higher Clinical Global Impressions-Severity (CGI-S) scores (6.0 -0.9 vs. 5.5 -0.8, p = 0.0018) and lower Children's Global Assessment Scale (CGAS) scores (29.6 -9.2 vs. 36.1 -8.9, p = 0.0002) and were more likely to be in the severely ill CGAS group (i.e., CGAS £ 40). SCZ-S and PsyNOS patients did not differ regarding all-cause discontinuation (40.5 vs. 40.3%. p = 0.49), discontinuation because of adverse effects (12.2% vs. 12.4%, p = 0.97), or nonadherence (29.3% vs. 30.9%, p = 0.88), but somewhat more SCZ-S patients discontinued treatment for inefficacy (19.5% vs. 7.4%, p = 0.063). CGI-S and CGAS scores improved significantly in both diagnostic groups ( p = 0.0001, each). Adjusting for baseline differences, PsyNOS patients experienced significantly better CGI-I improvement (CGI-I) scores ( p = 0.012) and more frequently reached higher categorical CGAS group status ( p = 0.021) than SCZ-S patients. Conclusions: Both youth with SCZ-S and those with PsyNOS experienced significant improvements with clinician's choice antipsychotic treatment. However, treatment discontinuation was common within 12 weeks, with greater inefficacy-related discontinuation in the SCZ-S group, whereas CGI-I and CGAS score-based improvements were greater in the PsyNOS group.