Flash droughts cause rapid depletion in root-zone soil moisture and severely affect crop health and irrigation water demands. However, their occurrence and impacts in the current and future climate in India remain unknown. Here we use observations and model simulations from the large ensemble of Community Earth System Model to quantify the risk of flash droughts in India. Root-zone soil moisture simulations conducted using Variable Infiltration Capacity model show that flash droughts predominantly occur during the summer monsoon season (June–September) and driven by the intraseasonal variability of monsoon rainfall. Positive temperature anomalies during the monsoon break rapidly deplete soil moisture, which is further exacerbated by the land-atmospheric feedback. The worst flash drought in the observed (1951–2016) climate occurred in 1979, affecting more than 40% of the country. The frequency of concurrent hot and dry extremes is projected to rise by about five-fold, causing approximately seven-fold increase in flash droughts like 1979 by the end of the 21st century. The increased risk of flash droughts in the future is attributed to intraseasonal variability of the summer monsoon rainfall and anthropogenic warming, which can have deleterious implications for crop production, irrigation demands and groundwater abstraction in India.