Pedestrian dead reckoning (PDR) is an effective positioning means that can be used in urban-canyon environments where the accuracy of GPS is significantly degraded. Magnetic disturbances caused by artificial objects affect the accuracy of positioning if the PDR system uses a magnetometer to estimate the heading direction. Conventional PDR systems consider magnetic disturbances as unpredictable error sources, but the error becomes predictable and removable if the amount of the deviation in the magnetic field can be calculated at any position. In this study, we propose a method to correct the heading direction by referring to a map of magnetic deviation. The experimental results show that our method reduced the error in the heading direction caused by magnetic disturbances. Our approach removed the error components that differ depending on the position, and consequently, the resultant trajectory represented better the shape of the true trajectory.