Aerobic exercise, training to sustain motor ability, and respiratory rehabilitation may improve general functioning and quality of life (QoL) in neuromuscular disorders. Patients with late-onset Pompe disease (LOPD) typically show progressive muscle weakness, respiratory dysfunction and minor cardiac involvement. Characteristics and modalities of motor and respiratory rehabilitation in LOPD are not well defined and specific guidelines are lacking. Therefore, we evaluated the role of physical activity, therapeutic exercise, and pulmonary rehabilitation programs in order to promote an appropriate management of motor and respiratory dysfunctions and improve QoL in patients with LOPD. We propose two operational protocols: one for an adapted physical activity (APA) plan and the other for an individual rehabilitation plan, particularly focused on therapeutic exercise (TE) and respiratory rehabilitation.