In this paper, we propose a new near infra-red (IR) vision-based gaze tracking method, which is not affected by facial movements in stereoscopic virtual reality (VR) systems. Our proposed method has following five novelties compared to previous works. (i) By using our gaze tracker instead of a conventional input device, users felt more interested and immersed in the stereoscopic VR system, (ii) by using an IR light passing filter and an IR illuminator, we were able to implement a robust gaze tracker irrespective of environmental lighting conditions, (iii) we used the simple 2D based eye and face gaze estimation method without considering the complicated 3D structure and motion of human eye and face, which could reduce the system complexities, (iv) to prevent the unintended movement of gaze position by natural eye blinking, we discriminated the eye blinking by measuring pupil size. And this information was used for button clicking and mode toggling based on the analysis of user's fatigue. That is, the measured fatigue information of user was used for the mode toggling between gaze tracking mode and the conventional mouse input mode, (v) the proposed method allowed the natural movement of user's head by tracking the IR rhombus-shaped pattern, which was not affected by the change of environmental lighting.Experimental results showed that the gaze estimation accuracy of the proposed method was 0.98 degrees. In addition, the subjective tests showed that the VR application using the proposed method was more interesting and immersive to users than those using conventional input devices.