Abstract Background Non-alcoholic fatty liver disease (NAFLD) is associated with endothelial dysfunction which is a common problem in haemodialysis patients and risk for high cardiovascular mortality in haemodialysis. Thrombomodulin is a promising marker of endothelial cell injury in different pathological conditions. This study evaluates the additive effect of non-alcoholic fatty liver disease (NAFLD) in prevalent HD (hemodialysis) patients on endothelial dysfunction. Methods This is a case-control study which was conducted on 60 ESRD (end-stage renal disease) patients on conventional hemodialysis and 30 apparently healthy controls. Patients were divided into 2 groups: group A (N = 30): with NAFLD& group B (N = 30): without NAFLD, excluding elderly, diabetic, chronic liver disease, advanced heart failure, active infection, COVID-19 infection and autoimmune disease& patients withhemodialysiscatheters. Thrombomodulin was measured for all participants by ELISA technique. Results Thrombomodulin had the ability to detect endothelial dysfunction in patients with NAFLD at Cut off value <0.8 ng/ml with sensitivity 53.33, specificity 80, PPV 72.7 and NPV 63.2. On comparing Thrombomodulin in patients with NAFLD(4.378±3.762 ng/ml), Non NAFLD (1.126±0.591 ng/ml)and control (0.755±0.314ng/ml) there was significant difference (P- value<0.001). Post hoc analysis showed significantly high Thrombomodulin level in patients with NAFLD compared to Non NAFLD and control with p-value<0.001 while there was no significant difference between patients with (Non NAFLD and control) p-value 0.792. NAFLD patients with higher Thrombomodulin level have 2.5 times higher risk to have endothelial dysfunction. There was no significant correlation between Thrombomodulin and all variables in the study. Conclusions Thrombomodulin can be used as specific marker for endothelial dysfunction in hemodialysis patients with Non Alcoholic fatty liver.