A new mechanistic cutting force model for flat end milling using the instantaneous cutting force coefficients is proposed. An in-depth analysis shows that the total cutting forces can be separated into two terms: a nominal component independent of the runout and a perturbation component induced by the runout. The instantaneous value of the nominal component is used to calibrate the cutting force coefficients. With the help of the perturbation component and the cutting force coefficients obtained above, the cutter runout is identified. Based on simulation and experimental results, the validity of the identification approach is demonstrated. The advantage of the proposed method lies in that the calibration performed with data of one cutting test under a specific regime can be applied for a great range of cutting conditions. A new mechanistic cutting force model for flat end milling using the instantaneous cutting force coefficients is proposed. An in-depth analysis shows that the total cutting forces can be separated into two terms: a nominal component independent of the runout and a perturbation component induced by the runout. The instantaneous value of the nominal component is used to calibrate the cutting force coefficients. With the help of the perturbation component and the cutting force coefficients obtained above, the cutter runout is identified. Based on simulation and experimental results, the validity of the identification approach is demonstrated. The advantage of the proposed method lies in that the calibration performed with data of one cutting test under a specific regime can be applied for a great range of cutting conditions.