Health related quality of life (HRQL) assessments during therapy for pediatric cancer are important. The objective of this study was to describe reasons for failure to provide HRQL assessments during a pediatric acute myeloid leukemia (AML) clinical trial. We focused on HRQL assessments embedded in a multicenter pediatric AML clinical trial. The PedsQL 4.0 Generic Core Scales, PedsQL 3.0 Acute Cancer Module, PedsQL Multidimensional Fatigue Scale, and Pediatric Inventory for Parents were obtained from parent/guardian respondents at a maximum of six time points. Children provided self-report optionally. A central study coordinator contacted sites with delinquent HRQL data. Reasons for failure to submit the HRQL assessments were evaluated by three pediatric oncologists and themes were generated using thematic analysis. There were 906 completed and 1091 potential assessments included in this analysis (83%). The median age of included children was 12.9 years (range 2.0 to 18.9). The five themes for non-completion were: patient too ill; passive or active refusal by respondent; developmental delay; logistical challenges; and poor knowledge of study processes from both the respondent and institutional perspective. We identified reasons for non-completion of HRQL assessments during active therapy. This information will facilitate recommendations to improve study processes and future HRQL study designs to maximize response rates.