To improve the accuracy of permanent magnet (PM) rotor position estimation for a hybrid stepper motor (HSM), the authors propose a sensorless control design based on the back electromagnetic force (back-EMF) caused by magnetic induction and harmonic rejection via an orthogonal third-order phase-locked loop (PLL3rd) and an integral harmonic filter (IHF). The accuracy of estimation is analysed considering PM rotor position estimation errors. The harmonics of the back-EMF signal are eliminated by the IHF before entering the PLL3rd, which synchronises and decreases position estimation error. This technique is a simple, reliable, and effective method for implementing sensorless control of an HSM. An industrial test-bench was used to implement the proposed scheme. The experimental results are presented to validate the effectiveness of the proposed estimation method.