Systems and methods for electromagnetic (EM) distortion detection and compensation are disclosed. In one aspect, the system includes an instrument, the system configured to: determine a reference position of the distal end of the instrument at a first time based on EM location data, determine that the distal end of the instrument at a second time is static, and determine that the EM location data at the second time is indicative of a position of the distal end of the instrument having changed from the reference position by greater than a threshold distance. The system is further configured to: determine a current offset based on the distance between the position at the second time and the reference position at the first time, and determine a compensated position of the distal end of the instrument based on the EM location data and the current offset.