Background: Anatomy apps supplement traditional learning; however, it is unknown if their use can improve students' outcome. The present study examined whether the use of anatomy apps improved student performance on a neuroanatomy assessment. Methods: Second-year anatomy students, enrolled in a Bachelor of Science with Chiropractic Major program, were randomly allocated to experimental and control groups in July 2015. Students completed the Self-Directed Learning Readiness Scale (SDLRS). The experimental group had access to iPads with four anatomy apps for three weekly classes (1.5 h each). One week after the last class, students were assessed by an online 30-question neuroanatomy test. Linear regression was used to examine the association between test scores and app use, gender, previous anatomy unit score and SDLRS scores. Students' views on apps were collected by focus group discussion immediately after the test. Results: Completed questionnaires were obtained from n = 25 control and n = 25 experimental students. There was no association between app use and neuroanatomy assessment score (B = 1.75, 95 % CI: -0.340-3.840, p = 0.099). Only previous anatomy unit score (B = 0.348, 95 % CI: 0.214-0.483, p < 0.001) affected neuroanatomy assessment scores. Students favored apps with clinical images and features including identification pins, sliding bars and rotatable 3D images. Conclusions: App use did not enhance learning outcomes in a second-year anatomy unit.