Virtual reality (VR) is projected to play an important role in education by increasing student engagement and motivation. However, little is known about the impact and utility of immersive VR for administering e-learning tools, or the underlying mechanisms that impact learners’ emotional processes while learning. This paper explores whether differences exist with regard to using either immersive or desktop VR to administer a virtual science learning simulation. We also investigate how the level of immersion impacts perceived learning outcomes using structural equation modeling. The sample consisted of 104 university students (39 females). Significantly higher scores were obtained on 11 of the 13 variables investigated using the immersive VR version of the simulation, with the largest differences occurring with regard to presence and motivation. Furthermore, we identified a model with two general paths by which immersion in VR impacts perceived learning outcomes. Specifically, we discovered an affective path in which immersion predicted presence and positive emotions, and a cognitive path in which immersion fostered a positive cognitive value of the task in line with the control value theory of achievement emotions.