As the electrification of the automotive industry accelerates, the importance of small-scale motors used in applications such as HVAC systems and water pumps is growing. To design small motors that exhibit high efficiency and high output within limited spaces, applying axial flux motors (AFMs) instead of conventional radial flux motors (RFMs) can maximize the power density within the same volume, offering advantages in both weight reduction and miniaturization. This study proposes an optimized end-turn layout design to mitigate back-EMF imbalance in AFMs utilizing PCB stators. Optimization results demonstrated that the structure employing a non-adjacent end-turn layout with equalized average end-turn heights (BCAACB type) exhibited the best performance in terms of average resistance and phase resistance variance, effectively mitigating back-EMF imbalance. The validity of the optimized end-turn structure was verified through finite element analysis (FEA). The analysis confirmed that the motor’s back-EMF balance was improved, and the magnitude of phase resistance was reduced. This reduction led to lower copper loss, thereby increasing overall efficiency. Furthermore, the variance in resistance for each phase was minimized, resulting in enhanced electrical balance. The results of this study are expected to contribute to enhancing the applicability of PCB stators in small motor design.