This work provides an innovative solution for monitoring fatigue for users behind workstations. A web camera was adjusted to work in near infrared range and a system of 880 nm IR diodes was implemented to create an IR vision system to localize and track the eye pupils. The software developed monitors and tracks eyes for signs of fatigue by measuring PERCLOS. The software developed runs on the workstation and is designed to draw limited computational power, so as to not interfere with the user task. To overcome low-frame rate imposed by the hardware limitations and to improve real time monitoring, two-phases detection and tacking algorithm is implemented. The proposed system successfully monitors fatigue at a rate of 8 fps. The system is well suited to monitor users in command centers, flight control centers, airport traffic dispatches, military operation and command centers, etc., but the work can be extended to wearable devices and other environments.