Late-onset Pompe disease (LOPD) is overwhelmingly caused by a single mutation that disrupts splicing of acid-alpha glucosidase (GAA) and results in the accumulation of lysosomal glycogen in muscle cells leading to progressive muscle weakness in patients. Current therapeutics for LOPD do not meet the needs of patients and have largely been developed in mutant animal models lacking Gaa expression, which more closely mimic the less common infantile form of the disease. Here we design and evaluate peptide-conjugated phosphorodiamidate morpholino oligomers (PPMOs) to target the causative mutation in GAA and correct pathogenic splicing in muscle tissue. We show PPMO compounds correct LOPD splicing in both patient induced pluripotent stem cell-derived muscle cells and in skeletal muscle tissue after intravenous dosing in a newly developed humanized LOPD animal model that recapitulates patient LOPD splicing.