Tracking the pose of an ultrasound (US) probe is essential for an intraoperative US-based navigation system. The tracking requires mounting a marker on the US probe and calibrating the probe. The goal of the US probe calibration is to determine the rigid transformation between the coordinate system (CS) of the image and the CS of the marker mounted on the probe. We present a fast and automatic calibration method based on a 3D printed phantom and an untracked marker for three-dimensional (3D) US probe calibration. To simplify the conventional calibration procedures using and tracking at least two markers, we used only one marker and did not track it in the whole calibration process. Our automatic calibration method is fast, simple and does not require any experience from the user. The performance of our calibration method was evaluated by point reconstruction tests. The root mean square (RMS) of the point reconstruction errors was 1.39 mm.