The Severe Acute Respiratory Syndrome (SARS) and Middle East Respiratory Syndrome (MERS) are two coronaviruses that have generated substantial nosocomial outbreaks. In particular, MERS continues to pose a significant threat in the Middle East since 2002. Currently, no licensed vaccine or drug treatment is available to treat patients infected with either virus. However, there are some MERS vaccines in the preclinical stage of development. We sought to evaluate the potential impact of targeted vaccination strategies for mitigating SARS and MERS outbreaks in healthcare settings by using simple statistical methods and detailed transmission trees describing the progression of prior nosocomial outbreaks. Our proposed vaccine strategies target two groups, patients and healthcare workers, who have contributed disproportionately to transmission. We assumed vaccination coverage levels at 50% and 75%. Our study found that vaccine strategies targeting patients averted nearly 50% of MERS and SARS. Thus, considering that SARS and MERS are amplified in healthcare settings due to diagnostic delays and suboptimal infection control measures, which facilitate the generation of super-spreading events, our results suggest that implementing a vaccine deployment strategy targeting patients has the potential to substantially limit transmission in the healthcare setting.