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Aim: To elucidate the effects of whole-body exercise on clinical outcomes, including dysphagia status, between stroke patients with dysphagia who are undergoing convalescent rehabilitation. Methods: This retrospective cohort study included consecutive patients with post-stroke dysphagia in a rehabilitation hospital in Japan between 2016 and 2018. Dysphagia was defined as a Food Intake Level Scale (FILS) score <7. Participants were asked to perform a repeated chair-stand exercise as a whole-body exercise in addition to the convalescence rehabilitation program. Study outcomes included the FILS score and presence of dysphagia at discharge, the Functional Independence Measure-motor (FIM-motor) score and length of stay. Multivariate analyses were used to determine whether the frequency of daily chair-stand exercise was independently associated with study outcomes, after adjusting for potential confounders; P < 0.05 was considered statistically significant. Results: Of the 637 patients admitted, 148 stroke patients with dysphagia (mean age 72.7 years; 48.6% men) were included in the final analysis dataset. The median daily frequency of repeated chair-stand exercise was 36 (12-65). In multivariate analyses, the frequency of chair-stand exercise was independently associated with the FILS score at discharge (β = 0.231, P = 0.015), the presence of dysphagia at discharge (odds ratio: 0.982, P = 0.035), FIM-motor at discharge (β = 0.205, P = 0.008) and its gain (β = 0.237, P = 0.013), and length of hospital stay (β = −0.042, P < 0.001). Conclusions: Chair-stand exercise is associated with preferable clinical outcomes, including dysphagia status, activities of daily living and length of hospital stay, in stroke patients with dysphagia. Post-stroke dysphagia rehabilitation should include whole-body exercises in addition to conventional rehabilitation programs.