Cutter runout will redistribute the instantaneous uncut chip thickness and the cutting forces in multi-fluted milling process. In this paper, a new procedure is proposed to identify the cutter runout parameters for flat end milling process. By combining least-square method, mathematical derivations and implementation procedures are carried out based on the relative deviation between each cutting edge and the spindle rotation center, measured by a dial gauge. Numerical verifications are conducted to validate the proposed procedures, and the results show that they are efficient and reliable. It is also suggested that to weaken the influence of noise signal, measurements should be conducted at multiple axial positions.