The high turnover rate of hospital pharmacists in Korea threatens patient safety. This study examined factors influencing turnover intentions and proposed retention strategies. A cross-sectional survey was conducted in July 2024 among pharmacists in tertiary and general hospitals, incorporating Mitchell’s Job Embeddedness Theory, the Korean Occupational Stress Scale, and Donnelly’s Turnover Intention Scale. Multivariate logistic regression identified significant factors associated with turnover intentions. Among 592 respondents, 255 (43.1%) had high turnover intentions. Key job embeddedness factors that reduced turnover intention included organizational fit (aOR 0.22, 95% CI 0.14–0.35), organization-related sacrifice (aOR 0.25, 95% CI 0.16–0.38), task-related organizational link (aOR 0.58, 95% CI 0.36–0.93), and community link (aOR 0.60, 95% CI 0.38–0.95). Conversely, turnover was significantly associated with job stress factors, including lack of reward (aOR 3.76, 95% CI 2.41–5.85), job demand (aOR 2.17, 95% CI 1.39–3.37), and organizational system fairness (aOR 1.61, 95% CI 1.01–2.57). This study suggests reducing turnover intentions among hospital pharmacists requires addressing organizational factors within job embeddedness and job stress, including lack of reward, job demand, and inadequacies in the organizational system. Strategies such as enhancing compensation, human resource management, and personnel systems are critical to retaining hospital pharmacists.