A pediatric implantable rotary blood pump (RBP) is under development in a research collaboration between the ETH Zurich, the University of Innsbruck, the University Medical Center Hamburg-Eppendorf and the Medical University of Vienna, in order to assist the Fontan circulation in newborns with a single ventricle. The RBP is driven by a small bearingless double-stator axial-flux permanent magnet synchronous machine, providing 2.2 mNm of torque at a rotational speed of 5500 rpm. The paper tackles the crucial challenge of defining an axial/angular position measurement concept with adequate resolution and bandwidth to enable magnetic levitation. As the sensors are integrated close the motor’s winding, the measurement signals are significantly disturbed by stray fields generated by the phase currents. Such disturbances are compensated to obtain a usable signal for closed-loop position control. The experimental results show that, with the proposed compensation, the measurement errors are reduced to only 45 μm and 2.2°.