This study is initial experiences in the design and evaluation of a serious game to supplement pupils’ understanding of molecular structures in chemistry. 27 pupils were included in the study, aged 13–14, with 16 boys and 11 girls. All participants were recruited from two chemistry classes at a Danish elementary school in Copenhagen. A formative evaluation consisted of both a questionnaire, observations, and interviews. The questionnaire was inspired by the User Engagement Scale (UES) short-form. Designing a serious game for pupils with the aim to increase the understanding of molecular structures, is not an easy task. This serious game was to some extend able to engage the pupils within the subject of chemistry. The game itself was reported to be very engaging, but the specific learning outcomes remains uncertain. We can conclude that the serious game was visually appealing, the pupils were absorbed in the game, and wanted to continue playing. However, the designed serious game was also a bit confusing and made too difficult, resulting in frustrations for the pupils. Further, there are still some important challenges in how to increase the validity and reliability when evaluating serious games with children and adolescent as the users.