The diagnosis of late-onset (childhood and adult) Pompe disease can often be challenging, as it is a rare disease and the heterogeneous clinical presentation can mimic the presentation of other neuromuscular disorders. The objective was to develop a consensus-based algorithm for the diagnosis of late-onset Pompe disease. A systematic literature search was conducted, and an expert panel composed of neuromuscular specialists and individuals with expertise in Pompe disease reviewed the literature and convened for consensus development. An algorithm for the diagnosis of late-onset Pompe disease was created. Patients presenting with either a limb-girdle syndrome or dyspnea secondary to diaphragm weakness should undergo further testing, including evaluations of muscle strength, motor function, and pulmonary function. A blood-based acid alpha-glucosidase (GAA) enzyme activity assay is the recommended tool to screen for GAA enzyme deficiency. The diagnosis should be confirmed by a second test: either a second GAA enzyme activity assay in another tissue or GAA gene sequencing.