Enterocytozoon hepatopenaei (EHP) is endemic in major shrimp farming countries affecting the economic sustainability, production and supply of shrimp in the global market. The study reports development of a stochastic model to estimate the economic loss due to EHP to Indian Penaeus vannamei shrimp farms and identify the associated key risk factors at the farm-level. Information on the cost of production and revenue were collected through a survey of shrimp farms (n = 281) from September to November 2020. The quantitative risk analysis for specific effects of the disease was estimated by Monte Carlo simulation using excel@Risk. The occurrence of the EHP was found to be positively correlated with the stocking density. The observed harvest of lower size shrimp and higher FCR could be attributed to EHP. Biological loss due to EHP was 75.21% and was highly significant. The cost of prevention of EHP was 15.22% and the treatment cost was 4.30%, along with an extraordinary cost of 5.26% with an average loss of ₹ 61,778 (US$ 813) ton−1 at farm-level. Regression sensitivity analysis revealed farm gate price was the strongest stochastic variable and one unit increase in farm gate price of shrimp positively influenced the net return by 0.76 units. The significant factors negatively influencing the net returns were expenditure on feed (0.51), seed (0.19) and labour (0.18). The net return estimated using Monte Carlo simulation in EHP affected farms was ₹ 14,390 (US$ 189.37) and the distribution revealed that nearly half of the farmers could lose their investment due to EHP. The study quantified the economic impact of EHP at the farm-level and identified the regional variation in the risk factors impacting the cost-benefit analysis of Indian shrimp farming. •Economic loss due to Enterocytozoon hepatopenaei (EHP) and associated risk factors were analyzed with stochastic model.•The disease caused an average loss of ₹ 61,778 (US$ 813) ton−1 of production.•Occurrence of the disease was positively correlated with stocking density.•Farm gate price was the positive variable while cost of feed, seed and labour negatively influenced the net returns.•Regional variation in the risk factors impacting the cost-benefit analysis was observed.