Abstract This paper concerns the stabilization problem for an underactuated robot called the Pendubot. Relying on a computational algorithm which is based on various results of the ‘polynomial matrix approach’, we propose an output-feedback-based internally stabilizing controller to stabilize the Pendubot at the unstable vertical upright position. The algorithm utilizes results for the solution of polynomial matrix Diophantine equations required for the computation and parameterization of proper ‘denominator assigning’ and internally stabilizing controllers for linear time invariant multivariable systems and reduces the problem to that of the solution of a set of numerical linear equations. The controller presented uses only the measured output which consists of the angles of the two links and does not require knowledge of the angular velocities which are usually not directly measurable. Comparative simulations are carried out to verify the good performance of the proposed controller. Finally, experimental results are provided to demonstrate the validity and feasibility of the proposed method.