This study examines the effect of surface currents on the bulk algorithm calculation of wind stress estimated using the scatterometer data during 2007-2020 in the Indian Ocean. In the study region as a whole the wind stress decreased by 5.4% by including currents into the wind stress equation. The most significant reduction in the wind stress is found along the most energetic regions with strong currents such as Somali Current, Equatorial Jets and Aghulhas retroflection. A highest reduction of 11.5% is observed along the equator where the Equatorial Jets prevail. A sensitivity analysis has been carried out for the study region and for different seasons to assess the relative impact of winds and currents in the estimation of wind stress by changing the winds while keeping the currents constants and vice versa. The inclusion of currents decreased the wind stress and this decrease is prominent when the currents are stronger. This study showed that equatorial Indian Ocean is the most sensitive region where the current can impact on wind stress estimation. The results showed that uncertainties in the wind stress estimations are quite large at regional levels and hence better representation of wind stress incorporating ocean currents should be considered in the ocean/climatic models for accurate air-sea interaction studies.