According to the resource of error, the subpixel location error of the facula centroid has been classified as random error and system error. A simple and effective method is proposed to measure the location error of facula centroid. A measuring system which mainly consists of a high precision motorized translation stage of one dimension, POINT GREY Flea2-14S3 CCD camera and LED light source was designed and constructed. Based on a detailed analysis for experiment results, the periodic changing law of system error of LED facula centroid location in this measuring system was found. The results indicate that based on Flea2-14S3 CCD camera, the random error of facula centroid location is about 0.018 pixels, the system error is about 0.06 pixels, and the total error is about 0.063 pixels (1/15 pixels). According to the total error above, this CCD imager can be widely used in many measuring systems which count on facula centroid subpixel detection. The experiment shows that the measuring system is an effective means to estimate the location error of facula centroid.