Common-mode chokes (CMC) are fundamental in electromagnetic interference (EMI) filters. 3-D simulation is becoming more and more important in recent years as it can take into account some effects that circuit modeling does not consider, such as the surrounding environment of the CMC. This paper investigates the influence of complex magnetic permeability on the 3-D simulation of a Mn-Zn CMC in its typical application frequency range (below 10 MHz). For this purpose, a simple method to extract complex permeability values by winding cores with a copper wire is applied. Then, the error in the extraction with different turn numbers is studied, and the setup to successfully perform a 3-D simulation of a Mn-Zn CMC is detailed. Finally, simulations of a commercial Mn-Zn CMC are performed up to 10 MHz to check the influence on electromagnetic simulations of complex permeability values extracted with different turn numbers.