In this study, an indirect method to estimate the setup runout of a ball-end mill from cutting force signal is proposed. This runout makes cutting forces of each tooth of the milling cutter unequal. By transforming the cutting force model from time domain to frequency domain through time-convolution theorem, the magnitude and phase angle of runout can be explicitly expressed with material constants, cutting conditions, and force signal. The static setup runout can be obtained by extrapolating estimated effective runout, which is independent of feedrate but decreases linearly with increase in axial depth of cut. The setup runout estimated by slot cutting experiments, shows good agreement with the measured one.