This paper presents a method to design the waveform of a back electromotive force (back EMF) of an axial flux permanent magnet (AFPM) motor using printed circuit board (PCB) windings. When the magnetization distribution of permanent magnet (PM) is given, the magnetic field in the air gap region is calculated by the quasi three dimensional (3D) space harmonic analysis (SHA) method. Once the flux density distribution in the winding region is determined, the required shape of the back EMF can be obtained by adjusting the winding distribution. This can be done by modifying the distance between patterns of PCB to control the harmonics in the winding distribution. The proposed method is verified by finite element analysis (FEA) results and it shows the usefulness of the method in eliminating a specific harmonic component in the back EMF waveform of a motor.