A goal of K-12 science education is for learners to develop scientific literacy. However, realizing this goal is being complicated by the availability of abundant resources that vary strongly regarding their adherence to the Nature of Science principles, particularly regarding socio-scientific issues, such as, for instance, vaccination. It requires dedicated reasoning skills, often referred to as critical thinking, to assess and value the arguments regarding such issues. To stimulate critical thinking, we investigate the use of interactive concept cartoons. Instead of a single cartoon our instrument provides a sequence of concept cartoons. The cartoons are alternated with a diagram and concepts that learners have to place in the diagram, leading to a systems’ view on the subject matter. The instrument has been presented to teachers for expert review and evaluated in three classrooms (6th grade) of one school (70 learners). In this paper, we present the interactive concept cartoon instrument and report on the study. The results indicate that learners are engaged when working with the instrument and learn relevant knowledge regarding the subject matter and the Nature of Science.