The aim of the present study was to examine the usability and reliability of the HEPS quality checklist (Healthy Eating and Physical Activity in Schools), an instrument developed to assess the quality of school-based programmes on healthy eating and physical activity. With regard to usability, health promotion experts (n = 15) were asked to apply the HEPS quality checklist and to fill out a questionnaire about its comprehensibility and usability. To examine inter-rater reliability (IRR) a criteria-based selection of German school programmes on healthy eating and physical activity (n = 14) was randomly allocated to two programme pools and assessed independently by the authors. Results of the pilot testing revealed a high overall satisfaction with the HEPS quality checklist and a high willingness to use it or to recommend it to others. Furthermore, the checklist was perceived to be comprehensive and clearly structured. The assessment results of programme pool 1 revealed unsatisfactory Cohen’s Kappa coefficients (IRR) and moderate intra-class correlations (ICC). After the HEPS manual guide had been amended with regard to its anchoring, the results of programme pool 2 showed substantial improvements with regard to IRR and ICC. In summary, the adapted HEPS quality checklist is a usable and reliable instrument for the quality assessment of school-based programmes on healthy eating and physical activity. The findings suggest that the HEPS checklist should be applied by two sufficiently trained raters.