Typical fundus photography produces a two-dimensional image. This makes it difficult to observe the microvascular and neural abnormalities, because the depth of the image is missing. To provide depth appreciation, we develop a single-channel stereoscopic fundus video imaging system based on a rotating refractor. With respect to the pupil center, the rotating refractor laterally displaces the optical path and the illumination. This allows standard monocular fundus cameras to generate stereo-parallax and image disparity through sequential image acquisition. We optimize our imaging system, characterize the stereo-base, and image an eyeball model and a rabbit eye. When virtual realities are considered, our imaging system can be a simple yet efficient technique to provide depth perception in a virtual space that allows users to perceive abnormalities in the eye fundus.