Persistent asthma requires a daily controller medication. National Heart, Lung, and Blood Institute (NHLBI) guidelines and Healthcare Effectiveness Data and Information Set (HEDIS) quality measures are used to identify persistent asthma, the former method used by clinicians, and the latter by managed care organizations (MCOs). This study aims to determine the degree of agreement between these criteria in classifying pediatric persistent asthma. Asthmatic patients aged 5–18 years old in a university pediatric practice who were continuously enrolled with one MCO from January 1, 2012 to December 31, 2013 (Cohort 1: 329 patients) and January 1, 2013 to December 31, 2014 (Cohort 2: 212 patients) were identified. Subjects with at least one asthma visit were included. Independence of NHLBI and HEDIS criteria was determined by the McNemar test. Agreement was determined by confusion matrix analysis and Cohen kappa statistic with continuity correction. Agreement in controller assignment was 82% in Cohort 1 and 88% in Cohort 2. Agreement was fair in Cohort 1 (Cohen kappa = 0.364; 95% confidence interval [CI] = 0.217–0.511) and moderate in Cohort 2 (Cohen kappa = 0.447; 95% CI = 0.247–0.646). The HEDIS misclassified persistent asthma by 16.4% (95% CI: 11.5–21.2%) and 11.8% (95% CI: 6.8–16.7%) in Cohorts 1 and 2, respectively. NHLBI and HEDIS criteria show fair to moderate agreement; however, the HEDIS consistently misclassified persistent asthma, suggesting that it is a poor measure of practice performance.