Evidence on polypharmacy in patients with sarcopenia is lacking. We aimed to examine the association of polypharmacy with swallowing function and nutritional risk in post-stroke patient with sarcopenia. This retrospective cohort study included hospitalized patients diagnosed with sarcopenia who needed convalescent rehabilitation following stroke onset. Study outcomes were the Food Intake Level Scale (FILS) as dysphagia assessment and geriatric nutritional risk index (GNRI) as nutritional status at hospital discharge, respectively. To examine the impact of admission polypharmacy, multivariate linear regression analyses were used to determine whether the number of drugs prescribed at hospital admission was associated with these outcomes. As a result, of the 586 patients enrolled, 257 (mean age 79.3 years, 44.0% male) were diagnosed with sarcopenia and were finally analyzed high admission drug prescription numbers were independently associated with FILS (β = −0.133, p = 0.017) and GNRI (β = −0.145, p = 0.003) at hospital discharge, respectively. Polypharmacy is associated with dysphagia and malnutrition in post-stroke patients with sarcopenia. In addition to the combination of nutritional and exercise therapies, review and optimization of prescription medications may be warranted to treat sarcopenia in order to maximize improvement in outcomes for these patients.