Stem canker of pigeonpea is caused by Macrophomina phaseolina is a seed as well as soil borne necrotrophic fungal pathogens infect more than 284 plant species including monocot and dicots throughout the world. It is the most destructive disease and causing severe yield loss in major pigeonpea growing areas of North-Eastern Karnataka. As the disease is more prevalent during hot temperature of 30 to 35 °C and low soil moisture conditions causing huge losses to the pigeonpea production. By considering the importance of the crop and disease, estimation of yield loss due to stem canker of pigeonpea caused by Macrophomina phaseolina at different stages of crop growth was need of the hour, particularly in the pulse growing districts of North Eastern Karnataka. Yield loss due to stem canker is estimated by randomly selecting the plants showing stem canker symptoms using disease rating scale. Three major pigeonpea genotypes were selected (Maruthi, TS3R and GRG-811). Among all the three varieties, Maruthi Grade 5 (highly susceptible) plants recorded 514 kg per hectare which shows 40.61 per cent decrease in the yield compared to the healthy plant, In the variety TS3R Grade 5 plants (Highly susceptible) recorded 912 kg per hectare which shows 28.71 per cent decrease in the yield compared to the healthy plant, In the variety GRG-811 Grade 5 plants (Highly susceptible) recorded 904 kg per hectare which shows 34.25 per cent decrease in the yield compared to the healthy plant.