The human–computer interaction (HCI) design of educational technologies influences cognitive behaviour, so it is imperative to assess how different HCI strategies support intended behaviour. We developed a neuroscience-inspired game that trains children's use of “stopping-and-thinking” (S&T)—an inhibitory control-related behaviour—in the context of counterintuitive science problems. We tested the efficacy of four HCI features in supporting S&T: (1) a readiness mechanic, (2) motion cues, (3) colour cues, and (4) rewards/penalties. In a randomised eye-tracking trial with 45 7-to-8-year-olds, we found that the readiness mechanic increased S&T duration, that motion and colour cues proved equally effective at promoting S&T, that combining symbolic colour with the readiness mechanic may have a cumulative effect, and that rewards/penalties may have distracted children from S&T. Additionally, S&T duration was related to in-game performance. Our results underscore the importance of interdisciplinary approaches to educational technology research that actively investigates how HCI impacts intended learning behaviours.