Systemic lupus erythematosus (SLE) is a chronic autoimmune disorder that can impact any organ in the body. The pathophysiology of shrinking lung syndrome (SLS), a rare pulmonary complication of SLE, remains unknown. The objective of the current case series was to investigate the effects of inspiratory muscle training (IMT) on diaphragm thickness/mobility, respiratory muscle strength, peripheral muscle thickness/strength, and functional exercise capacity in patients with SLE and associated SLS. Three patients with SLE were included in the case series. Respiratory muscle strength, peripheral muscle strength, peripheral muscle thickness, diaphragm muscle thickness, diaphragm muscle mobility, functional exercise capacity, and pulmonary function test were assessed. A significant improvement has been determined in respiratory muscle strength, functional exercise capacity, peripheral muscle strength, peripheral muscle thickness, diaphragm muscle thickness, and diaphragm muscle mobility. This is the first case series showing the beneficial effects of IMT on respiratory muscle strength, diaphragm thickness/mobility, peripheral muscle thickness/strength, and exercise capacity in patients with SLE.