Confusion may benefit learning when it is resolved or partially resolved. Metacognitive strategies (MS) may help learners to resolve confusion when it occurs during learning and problem solving. This study examined the relationship between confusion and MS that students evoked in Betty's Brain, a computer-based learning-by-modelling environment where elementary and middle school students learn science by building causal maps. Participants were sixth graders. Emotion data were collected from real-time observations by trained researchers. MS and task performance information were determined by analyzing the action logs. Pre- and post-tests were used to assess learning gains. The results revealed that the use of MS was a function of the state of student confusion. However, confusion resolution was not related to MS behaviour, and MS did not moderate the effect of confusion on student task performance in Betty's Brain or on learning gains.