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A foot-mounted pedestrian dead reckoning system is a self-contained technique for indoor localization. An inertial pedestrian navigation system includes wearable MEMS inertial sensors, such as an accelerometer, gyroscope, or digital compass, which enable the measurement of the step length and the heading direction. Therefore, the use of zero velocity updates is necessary to minimize the inertial drift accumulation of the sensors. The aim of this paper is to develop a foot-mounted pedestrian dead reckoning system based on an inertial measurement unit and a permanent magnet. Our approach enables the stance phase and the step duration detection based on the measurements of the permanent magnet field during each gait cycle. The proposed system involves several parts: inertial state estimation, stance phase detection, altitude measurement, and error state Kalman Filter with zero velocity update and altitude measurement update. Real indoor experiments demonstrate that the proposed algorithm is capable of estimating the trajectory accurately with low estimation error.