Crop Yield Loss (CYL) due to surface ozone substantially affects the Indian economy and the food availability for a billion residents. Nevertheless, the incurring losses over India remain uncertain due to limited measurements and significant uncertainties in the surface O3 simulated by chemistry-transport models, amongst other causes. Here, we revisit the ozone-attributable CYL using WRF-Chem model, with a set up previously shown to better reproduce the observed ozone variations over the contrasting chemical environments across the Indian region. WRF-Chem simulated ozone fields are converted to Accumulated Ozone above a Threshold of 40 ppbv (AOT40) for two primary crop growing seasons in India, i.e. Kharif (mid-June to mid-September), and Rabi (December to February). Relative Yield Losses (RYL) for wheat are found to be higher (∼21–26%) than those in a recent study based on observations (∼15%), as the model accounts for the rural chemistry which can be different from urban/suburban/high altitude environments where measurements are largely conducted. Additionally, RYL for rice estimated here (∼6%) is 3 times greater than a previous study using this model at a relatively coarser resolution to derive average surface ozone with a set of simulations with varying emission inventories, not evaluated in detail before deriving crop losses. The economic losses due to CYL estimated in this study (∼5 billion USD for wheat and 1.5 billion USD for rice) are on the higher side, when estimations from various studies are inter-compared (0.6–4.3 billion USD for wheat, and 0.5–1.5 billion USD for rice), for which increasing crop prices is also a contributing factor. Our study highlights an urgent need to conduct strategic ozone observations especially over agricultural fields, and the development of yearly regional-emission database to support policy making in India. © 2019 The Authors