Many drought indices are available for quantifying and characterizing the drought events. Selection of a particular drought index could influence the outcome of the study. In this study, we compared two drought indices namely, Standardized precipitation index (SPI) and Standardized Precipitation-Evapotranspiration Index (SPEI) under climate change condition. Data from 7 RCM models namely, CCCma-CanESM2, CERFACS-CNRM-CM5, GFDL-ESM2M, MOHC-HadGEM2, MIROC-MIROC5, MPI-ESM-LR and MPI-ESM-MR for RCP 4.5 scenario have been used to calculate 12 month SPI and SPEI values. L-moments which provides robust distribution parameter estimation, have been used to identify best fit distribution for projected data at each grid point for each month. Mann-Kendall and Sen's slope test have been used to detect trends in drought severity, duration, peak, and interval between drought events. Results of this study reveal that SPI shows decreasing trends in drought severity, duration and peak with negative Sen's slope, however, the SPEI shows increasing trends of severity, duration and peak with a positive Sen's slope for almost all over India. The analysis reveals that projected percentage of drought affected area based on SPI in the first half of the 21st century is higher compared to those obtained using SPEI, however for the second half of the 21st century, the projected drought affected computed using SPEI is higher compared to the corresponding area obtained using SPI. Decrease in droughts severity, duration and peaks in SPI analysis could be attributed to projected increase in monsoon rainfall in Indian Subcontinent during second half of 21st century however, SPI was found incapable to account the increase in temperature thus neglecting the drying due to increased evapotranspiration whereas SPEI shows significant drying in Indian subcontinent on account of increasing trend in temperature observed in projected future RCM scenarios.