Objectives: To describe medication management of children diagnosed with anxiety and depression by primary care providers. Study Design/Methods: We performed a retrospective cross-sectional analysis of electronic health record (EHR) structured data. All visits for pediatric patients seen at least twice during a four-year period within a network of primary care clinics in Northern California were included. Descriptive statistics summarized patient variables and most commonly prescribed medications. For each subcohort (anxiety, depression, and both (anxiety+depression)), logistic regression models examined the variables associated with medication prescription. Results: Of all patients (N=93,025), 2.8% (n=2635) had a diagnosis of anxiety only, 1.5% (n=1433) depression only, and 0.79% (n=737) both anxiety and depression (anxiety+depression); 18% of children with anxiety and/or depression had comorbid ADHD. A total of 14.0% with anxiety (n=370), 20.3% with depression (n=291), and 47.5% with anxiety+depression (n=350) received a psychoactive non-stimulant medication. For anxiety only and depression only, sertraline, citalopram, and fluoxetine were most commonly prescribed. For anxiety+depression, citalopram, sertraline, and escitalopram were most commonly prescribed. The top prescribed medications also included benzodiazepines. Logistic regression models showed that older age and having developmental or mental health comorbidities were independently associated with increased likelihood of medication prescription for children with anxiety, depression, and anxiety+depression. Insurance type and sex were not associated with medication prescription. Conclusions: PCPs prescribe medications more frequently for patients with anxiety+depression than for patients with either diagnosis alone. Medication choices generally align with current recommendations. Future research should focus on the use of benzodiazepines due to safety concerns in children.