This case report describes the orthodontic treatment of a 9-year-old girl who presented with multiple agenesis, maxillary contraction, and skeletal Class III malocclusion after the surgical removal of a melanocytic neuroectodermal tumour of infancy (MNTI) or the so-called melanocytic progonoma at 40 days of age. The lack of dental anchorage in the posterior segment of the second quadrant and the search for maximum control during suture expansion to reduce dental effects led to the use of a hybrid rapid palatal expander (RPE) with dental anchorage in the first quadrant and skeletal anchorage on the two miniscrews placed in the second quadrant, to allow a more even distribution of expansion forces. The expansion procedures performed with the hybrid anchorage device and extraoral traction demonstrate the possibility of solving the contraction in the posterior segments and anterior crossbite in a few months with maximum control of the applied forces, despite the objective difficulties related to the specificity of the case.