Background Children with chronic kidney disease (CKD) are at risk for neurocognitive deficits while simultaneously being at risk for chronic school absenteeism (≥ 18 school days per school year). Chronic school absenteeism compounds the negative impacts of CKD on academic achievement. In this study, we examined patient- and caregiver-reported factors associated with school absenteeism in children with non-dialysis- or transplant-dependent CKD in order to help identify which factors could be modifiable and ultimately improve school attendance. Methods We utilized a combination of chart review and questionnaires distributed in person to patients and caregivers at a pediatric nephrology clinic between November 2018 and August 2019 to gather data. We used descriptive statistics to illustrate clinical characteristics of the children included in the study, caregiver characteristics, and examined reported reasons for missing school. Results Twenty-one percent of participants (10/48) missed 18 full days of school or more, categorizing them as chronically absent. The top three reasons for missing school were doctor appointments, feeling sick, and being bullied. More specific sequelae of CKD were not highly reported as reasons for missing school. Conclusions Chronic absenteeism is a highly reported phenomenon among children with pediatric CKD. Given that missing school for doctor appointments was a top reason for absenteeism, this data suggests alternative appointment hours and virtual appointments may reduce chronic school absenteeism in children, and by extension improve their health, behavioral, and academic outcomes. Graphical abstract A higher resolution version of the Graphical abstract is available as Supplementary information Supplementary Information The online version contains supplementary material available at 10.1007/s00467-022-05780-2.