A five degrees-of-freedom overhead crane system affected by external perturbations is the topic of study. Existing methods just handle the unperturbed case or, in addition, the analysis is limited to three or two degrees-of-freedom. A wide range of processes cannot be restricted to these scenarios and this paper goes a step forward proposing a control solution for a five degrees-of-freedom system under the presence of matched and unmatched disturbances. The contribution includes a model description and a second-order sliding mode (SOSM) control design ensuring the precise trajectory tracking for the actuated variables and at the same time the regulation of the unactuated variables. Furthermore, the proposed approach is supported by the design of strong Lyapunov functions providing an estimation of the convergence time. Simulations and experiments, including a comparison with a proportional-integral-derivative (PID) controller, verified the advantages of the methodology.