Uncertainty in diopter measurement with eccentric photorefraction is analyzed. Major reasons that cause higher uncertainty, such as existing of transition region, blurring of pupil edge and difficulty to distinguish iris from darkspace, are pointed out. Calculation equation for uncertainty is derived and combined standard uncertainties of diopter of schematic eyes with different myopia are computed. A radical mean, that is, asking for a new direct measuring quantity instead of the vertical coordinates of high and low edges of darkspace is proposed.