The objective of this study is to assess (1) the concordance and validity of schizophrenia register diagnoses among children and adolescents (early onset schizophrenia = EOS) in the Danish Psychiatric Central Research Register (DPCRR), and (2) the validity of clinical record schizophrenia diagnoses. Psychiatric records from 200 patients with a first-time diagnosis of schizophrenia (F20.x) at age < 18 years between 1994 and 2009 in the DPCRR were rated by experienced clinicians according to ICD-10 criteria, using a predefined checklist. We retrieved 178 records, representing 19.6% of all patients diagnosed with EOS from 1994 to 2009. Mean age was 15.2 years and 56.2% were males. The register-based and clinical diagnoses matched in 158 cases (88.8%). Raters’ diagnoses confirmed the DPCRR schizophrenia diagnoses in 134 cases, rendering a diagnostic validity of 75.3% of DPCRR schizophrenia, while 149 cases were confirmed as being in the schizophrenia spectrum (83.7%). When removing records with registration errors, 83.5% of cases were confirmed as schizophrenia and 91.8% as being in the schizophrenia spectrum. Interrater reliability was substantial with Cohen’s kappa > 0.78–0.83 depending on classification. Compared to diagnoses made in outpatient settings, EOS diagnoses during hospitalizations were more likely to be valid and had fewer registration errors. Diagnosed in inpatient settings, EOS diagnoses are reliable and valid for register-based research. Schizophrenia diagnosed in children and adolescents in outpatient settings were found to have a high number of false-positives, both due to registration errors and diagnostic practice. Utilizing this knowledge, it is possible to reduce the number of false-positives in register-based research of EOS.