Although subjective global assessment (SGA) is a widely used representative tool for nutritional investigations even among dialysis patients, no studies have examined gender-specific differences in the ability of SGA to predict mortality in hemodialysis (HD) patients. A total of 2,798 dialysis patients were enrolled from clinical research center for end-stage renal disease (CRC for ESRD) between 2009 and 2015. The cohort was divided into two groups based on nutritional status as evaluated by SGA: ‘good nutrition’ and ‘mild to severe malnutrition’. Multivariate Cox proportional regression analyses were performed to investigate gender-specific differences in SGA for mortality among incident and prevalent HD patients. ‘Mild to severe malnutrition’ was significantly correlated with increased mortality compared with ‘good nutrition’ for all HD, incident and prevalent HD patients. Compared with ‘good nutrition’, ‘mild to severe malnutrition’ was also more significantly associated with increased mortality in male patients in the incident and prevalent HD groups. However, no significant associations between nutritional status evaluated by SGA and mortality were observed for female patients. SGA of HD patients can be useful for predicting mortality, especially in male HD patients. However, SGA alone might not reflect adverse outcomes in female patients.