Little is known about lone atrial fibrillation (AF) in pediatrics and its risk factors due to low prevalence. We sought to determine risk factors and estimate recurrence rates in children with lone AF using a large clinical database. Using the Explorys clinical database, we retrospectively identified patients who were below 20 years of age at the time of their AF diagnosis. Patients with congenital heart disease, cardiomyopathy, prior open heart surgery, or thyroid disease were excluded. Out of 7,969,230 children identified, 1910 had AF and 1570 met the definition of lone AF. The prevalence of lone AF was 7.5 per 100,000 children. In comparison to young children (0–4 years), risk for lone AF increased with age (adjusted odds ratio (aOR) 1.2 [95% CI 0.9–1.5, P = 0.21] in those 5–9 years, aOR 1.7 [95% CI 1.3–2.1, P < 0.001] in those 10–14 years, and aOR 10.7 [95% CI 8.7–13.2, P < 0.001] in those 15–19 years). Risk of lone AF was also higher in males than females (aOR 1.7 [95% CI 1.5–1.9, P < 0.001]), and was higher in obese children (BMI ≥ 95th percentile) versus children with normal BMI (aOR 1.3 [95% CI 1.1–1.5], P < 0.001), but there was no difference between overweight (BMI = 85th–94th percentile) and normal (P = 0.14). One-month recurrence rate was 15%, and increased with age. In this large pediatric cohort, the prevalence of lone AF was low, but risk was higher in males and increased with age and obesity. Older children with lone AF had higher rates of recurrence.