Application of modern technologies, including virtual reality (VR) and eye-tracking (ET), to educational practice has been vigorously researched over the past decade with a focus on enhancing and improving school and university educational process and students' results. The main aim of this technological report is to describe an implementation of a novel toolkit for tracking eye movements in a VR headset. The toolkit is implemented in Narupa iMD-an environment that allows visualizing molecular dynamics and interactions in VR for chemistry education. The toolkit is flexible and can be adapted to other VR environments and for subject areas other than chemistry. The HTC Vive Pro Eye was chosen as a head-mounted display (HMD) which supports eye-tracking. The toolkit is designed to primarily work with that device, but can be adapted to other HMDs with ET module. The current report describes a step-by-step process of developing and implementing the software to track eye movements during the learning process. We discuss future prospects for usage of this technology in research and educational practice.