With the increasing use of virtual reality (VR) technology in education, it is crucial to understand the factors that affect its effectiveness. One area where VR has been utilized is in online orientation, which can be especially beneficial for distant students to start their university programs. This study examines the impact of the learner attribute, behavioral engagement, on learning outcomes in a 3D desktop VR new student online orientation. Over 100 graduate and undergraduate students participated in the study and the results from regression analyses (n = 115) indicate a very weak positive relationship between engagement and learning outcomes (R = 0.0014, p = 0.98), with a negligible proportion of variance explained by engagement. The coefficient of engagement (−0.0066) suggests a negligible and non-significant effect on the dependent variable, indicating limited predictive power. While participants report high levels of perceived engagement, concentration, control, and skilfulness during the activity, they express difficulty viewing avatars in virtual world as real people. These findings have important implications for the development and implementation of VR-based educational interventions, highlighting the need to consider learners’ engagement.