In this study, we investigate the problem of tracking objects with unknown shapes using three-dimensional (3D) point cloud data. We propose a Gaussian process-based model to jointly estimate object kinematics, including position, velocity and orientation, together with the shape of the object in an online fashion. We describe the unknown shape by a radial function in 3D, and induce a correlation structure via a Gaussian process. Furthermore, we propose an efficient algorithm to reduce the computational complexity of working with 3D data. This is accomplished by casting the tracking problem into projection planes which are attached to the object's local frame. The proposed methods provide an analytical expression for the object shape together with confidence intervals. The confidence intervals, which quantify the uncertainty in the shape estimate, can later be used for solving the gating and association problems inherent in object tracking. The performance of the methods is demonstrated both on simulated and real data. The results are compared with an existing random matrix model, which is commonly used for extended object tracking in the literature.