Second-generation antipsychotic (SGA) prescription use has become increasingly prevalent in the pediatric population, despite metabolic adverse effects. A significant number of SGA medications are prescribed for indications that are not approved by the FDA. This study aimed to quantify clinician adherence to the FDA and professional society indication, age, and dosing guidelines when prescribing SGA medications for pediatric patients. We used electronic health record data from 3 health care systems. We analyzed outpatient encounters where a pediatric patient was prescribed an SGA during an 18-month time frame. Clinician prescribing patterns were compared to a therapeutic regimen table created using professional society guidelines and FDA medication labels. Most of the encounters listed an indication that was not documented as a recommended use (84.3%). Most prescriptions aligned with the generalized dose guidelines (93.8%) and age guidelines (94.9%). Clinicians were more likely to follow indication guidelines when prescribing risperidone, the highest adherence medication, compared with quetiapine, the lowest adherence medication (odds ratio [OR], 2.5; 95% CI, 1.1-6.0). Compared with prescriptions for younger children, clinicians were more likely to follow indication guidelines for children aged 13 to 15 years (OR, 2.8; 95% CI, 1.1-7.2) and 16 to 18 years (OR, 3.1; 95% CI, 1.2-8.1). Community clinicians overall demonstrated a low level of adherence to indication guidelines when prescribing SGA medications to pediatric populations, while maintaining higher adherence to age and dosing guidelines. Older children were more likely to receive an SGA prescription for recommended indications compared with younger children.