When accessing learning content designed using virtual reality (VR) technology, to observe a 3D object in detail, learners tend to bring the object closer to their eyes. However, this can cause visual fatigue because of the vergence–accommodation conflict (VAC) in stereoscopic viewing. While VR technology enables learners to move 3D objects freely, it is difficult to determine at what depth and for how long learners are viewing 3D content. Prolonged viewing at a near distance can result in severe visual fatigue. Consequently, this study aims to quantify VAC when using VR educational content to facilitate a comfortable learning experience. The authors of this study have developed a function to measure the viewing distance, the depth position of a 3D object, and the amount of binocular disparity when viewing VR educational content. The amount of binocular disparity indicates the degree of VAC. Consequently, estimation of the degree of induced visual fatigue becomes possible. Further, the developed function showed good accuracy. Time-series measurements can also be made using this function. Thus, this study provides a method to objectively record how learning with stereo images takes place, and further proposes ways to reduce the associated visual fatigue.