Purpose Health care‐associated infection (HAI) is costly to hospitals and potentially life‐threatening to patients. Numerous infection prevention programs have been implemented in hospitals across the United States. Yet, little is known about infection prevention practices and implementation in rural hospitals. The purpose of this study was to understand the infection prevention practices used by rural Veterans’ Affairs (VA) hospitals and the unique factors they face in implementing these practices. Methods This study used a sequential, mixed methods approach. Survey data to identify the HAI prevention practices used by rural VA hospitals were collected, analyzed, and used to inform the development of a semistructured interview guide. Phone interviews were conducted followed by site visits to rural VA hospitals. Findings We found that most rural VA hospitals were using key recommended infection prevention practices. Nonetheless, a number of challenges with practice implementation were identified. The 3 most prominent themes were: (1) lack of human capital including staff with HAI expertise; (2) having to cultivate needed resources; and (3) operating as a system within a system. Conclusions Rural VA hospitals are providing key infection prevention services to ensure a safe environment for the veterans they serve. However, certain factors, such as staff expertise, limited resources, and local context impacted how and when these practices were used. The creative use of more accessible alternative resources as well as greater flexibility in implementing HAI‐related initiatives may be important strategies to further improve delivery of these important services by rural VA hospitals.