COVID-19 infections can lead to worse outcomes in an immunocompromised population with multiple comorbidities, e.g., heart transplant patients. We used the National Inpatient Sample database to compare heart transplant outcomes in patients with COVID-19 vs. influenza. A total of 2460 patients were included in this study: heart transplant with COVID-19 (n = 1155, 47.0%) and heart transplant with influenza (n = 1305, 53.0%) with the primary outcome of in-hospital mortality. In-hospital mortality (n = 120) was significantly higher for heart transplant patients infected with COVID-19 compared to those infected with influenza (9.5% vs. 0.8%, adjusted OR: 51.6 [95% CI 4.3–615.9], p = 0.002) along with significantly higher rates of mechanical ventilation, acute heart failure, ventricular arrhythmias, and higher mean total hospitalization cost compared to the influenza group. More studies are needed on the role of vaccination and treatment to improve outcomes in this vulnerable population.