Abstract Background The adult versions EQ-5D-3L and EQ-5D-5L have been extensive compared. This is not the case for the EQ-5D youth versions. The study aim was to compare the measurement properties and responsiveness of EQ-5D-Y-3L and EQ-5D-Y-5L in paediatric patients. Methods A sample of patients 8–16 years old with different diseases and a wide range of disease severity was asked to complete EQ-5D-Y-3L, EQ-5D-Y-5L, PedsQL Generic Core Scale, and selected, appropriate disease-specific instruments, three times. EQ-5D-Y-3L and EQ-5D-Y-5L were compared in terms of: feasibility, (re-)distribution properties, discriminatory power, convergent validity, test–retest reliability, and responsiveness. Results 286 participating patients suffered from one of the following diseases: major beta-thalassemia, haemophilia, acute lymphoblastic leukaemia, acute illness. Missing responses were comparable between versions of the EQ-5D-Y, suggesting comparable feasibility. The number of patients in the best health state (level profile 11111) was equal in both EQ-5D-Y versions. The projection of EQ-5D-Y-3L scores onto EQ-5D-Y-5L for all dimensions showed that the two additional levels in EQ-5D-Y-5L slightly improved the accuracy of patients in reporting their problems, especially if severe. Convergent validity with PedsQL and disease-specific measures showed that the two EQ-5D-Y versions performed about equally. Test–retest reliability (EQ-5D-Y-3L 0.78 vs EQ-5D-Y-5L 0.84), and sensitivity for detecting health changes, were both better in EQ-5D-Y-5L. Conclusions Extending the number of levels did not give clear superiority to EQ-5D-Y-5L over EQ-5D-Y-3L based on the criteria assessed in this study. However, increasing the number of levels benefitted EQ-5D-Y performance in the measurement of moderate to severe problems and especially in longitudinal study designs.