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Abstract Background We sought to describe the burden of arrhythmias and their impact on in‐hospital outcomes in transgender patients who underwent gender re‐assignment surgery. Methods The study utilized data from the National Inpatient Sample from January 2012 to September 2015. Results 16 555 adult transgender patients were included in this study. A total of 610 adults developed arrhythmia out of which atrial fibrillation (N = 475, 2.87%) was the most frequent arrhythmia. In‐hospital mortality increased substantially with arrhythmias. Conclusions New‐onset arrythmias, while infrequent in the inpatient setting is associated with significantly higher in‐hospital mortality and resource utilization.