External and internal convertible (EIC) form-based motion control is one of the effective designs of simultaneously trajectory tracking and balance for underactuated balance robots. Under certain conditions, the EIC-based control design however leads to uncontrolled robot motion. We present a Gaussian process (GP)-based data-driven learning control for underactuated balance robots with the EIC modeling structure. Two GP-based learning controllers are presented by using the EIC structure property. The partial EIC (PEIC)-based control design partitions the robotic dynamics into a fully actuated subsystem and one reduced-order underactuated system. The null-space EIC (NEIC)-based control compensates for the uncontrolled motion in a subspace, while the other closed-loop dynamics are not affected. Under the PEIC- and NEIC-based, the tracking and balance tasks are guaranteed and convergence rate and bounded errors are achieved without causing any uncontrolled motion by the original EIC-based control. We validate the results and demonstrate the GP-based learning control design performance using two inverted pendulum platforms.