Background: In this study, we aimed to determine how school attendance changed over time for children on Medicaid with chronic health conditions enrolled in a comprehensive care coordination program called Coordinated HEalthcare for Complex Kids (CHECK). Methods: Medicaid beneficiaries from one managed care organization were randomized into 2 arms: CHECK program services or usual care. The final sample was 1322. Results: The mean age was 10.9 (SD = 3.7) years old and children were mostly non-Hispanic Black (62.6%) or Hispanic (34.9%). The median school attendance at baseline was 94.9% (IQR 88.9, 97.9); over one-fourth of children (28.4%) were chronically absent. School attendance was not associated with race/ethnicity, risk level, and health condition. In a model including a significant time/grade interaction, school attendance increased over time for children in pre-kindergarten (OR = 1.52, 95% CI: 1.38, 1.68; p < 0.001) and kindergarten to 5th grade (OR = 1.21, 95% CI: 1.17, 1.26; p < 0.001), and decreased for children in 6th to 8th grade (OR = 0.80, 95% CI: 0.77, 0.83; p < 0.001). No differences were seen in school attendance or chronic absenteeism associated with enrollment in the CHECK program. Conclusions: School attendance improved for most of the low-income children with chronic health conditions in our cohort, except for children in middle school.