The purpose of this study was to assess the prevalence and prognosis of cachexia in patients with non-sarcopenic dysphagia. A retrospective cohort study was conducted using the Japanese sarcopenic dysphagia database. Cachexia was diagnosed using the Asian Working Group for Cachexia criteria, sarcopenia using the Asian Working Group for Sarcopenia 2019 criteria, and malnutrition using the Global Leadership Initiative on Malnutrition criteria. Outcomes were death, swallowing function (Food Intake LEVEL Scale (FILS)), and activities of daily living (Barthel Index (BI)). The mean age of the 175 non-sarcopenic dysphagia patients was 77 (±11) years; 103 (59%) were male, 30 (17%) had cachexia, 133 (76%) had whole-body sarcopenia, and 92 (53%) were malnourished. Of the 30 patients with cachexia, 4 and 11 did not have sarcopenia and malnutrition, respectively. No significant associations were found between cachexia, sarcopenia, and malnutrition. Death was notably higher in the cachexia group (5/30; 17% vs. 2/145; 1%, p = 0.002). Median FILS (7 vs. 8, p = 0.585) and median BI (35 vs. 50, p = 0.469) scores did not show significant differences based on cachexia status. The prevalence of cachexia was 17%, and mortality may be higher with cachexia in non-sarcopenic dysphagia patients.