The EQ-5D-Y-3L is a generic, health-related, quality-of-life instrument for use in younger populations. Some methodological studies have explored the valuation of children’s EQ-5D-Y-3L health states. There are currently no published value sets available for the EQ-5D-Y-3L that are appropriate for use in a cost-utility analysis. The aim of this article was to describe the development of the valuation protocol for the EQ-5D-Y-3L instrument. There were several research questions that needed to be answered to develop a valuation protocol for EQ-5D-Y-3L health states. Most important of these were: (1) Do we need to obtain separate values for the EQ-5D-Y-3L, or can we use the ones from the EQ-5D-3L? (2) Whose values should we elicit: children or adults? (3) Which valuation methods should be used to obtain values for child’s health states that are anchored in Full health = 1 and Dead = 0? The EuroQol Research Foundation has pursued a research programme to provide insight into these questions. In this article, we summarized the results of the research programme concluding with the description of the features of the EQ-5D-Y-3L valuation protocol. The tasks included in the protocol for valuing EQ-5D-Y-3L health states are discrete choice experiments for obtaining the relative importance of dimensions/levels and composite time-trade-off for anchoring the discrete choice experiment values on 1 = Full Health and 0 = Dead. This protocol is now available for use by research teams to generate EQ-5D-Y-3L value sets for their countries allowing the implementation of a cost-utility analysis for younger populations.