Ultrasound imaging is a dynamic imaging technique that uses high‐frequency sound waves to capture live images of the structures beneath the skin. In addition to its growing use in diagnosis and interventions, ultrasound imaging has the potential to reinforce concepts in the undergraduate medical curriculum. However, research assessing the impact of ultrasound on anatomy learning and student cognition is scarce. The purpose of this study was to compare the impact of ultrasound‐based instruction versus narrated videos on students' understanding of anatomical relationships, as well as the role of intrinsic motivation, self‐efficacy beliefs, and students' attitudes in this process. A booster course on anterior leg and wrist anatomy was offered to second‐year medical students. A randomized controlled trial with a cross‐over design allocated students to either an ultrasound‐based teaching condition (cohort A) or a narrated anatomy video condition (cohort B). Next, participants were crossed to the alternative intervention. At the start of the study (T0), baseline anatomy knowledge, intrinsic motivation, self‐efficacy beliefs, and spatial ability were measured. After the first intervention (T1) and at the end of the study (T2), both cohorts were administered an anatomy test, an intrinsic motivation scale, and a self‐efficacy scale. In addition, each student was asked to fill out a perception survey after the ultrasound intervention. Finally, building on the cross‐over design, the most optimal sequence of interventions was examined. A total of 181 students participated (cohort A: n = 82, cohort B: n = 99). Both cohorts performed comparably on the baseline anatomy knowledge test, spatial ability test, intrinsic motivation, and self‐efficacy scale. At T1, cohort B outperformed cohort A on the anatomy test (p = 0.019), although only a small effect size could be detected (Cohen's d = 0.34). Intrinsic motivation and self‐efficacy of both cohorts were similar at T1. At T2, the anatomy test, intrinsic motivation, and self‐efficacy scale did not reflect an effect after studying either sequence of the interventions. Students reported favorably about the ultrasound experience, but also mentioned a steep learning curve. Medical students found the hands‐on ultrasound sessions to be valuable, increasing their interest in musculoskeletal anatomy and ultrasound imaging. However, the addition of ultrasound did not result in superior spatial anatomy understanding compared to watching anatomy videos. In addition, ultrasound teaching did not have a major effect on student cognition. Ultrasound‐based teaching of musculoskeletal anatomy is regarded as difficult to learn, and therefore it is hypothesized that too high levels of cognitive load might explain the presented results.