In recent decades the water resource of Nile river basin (NRB) has suffered from increasing demands from competing users, and global warming impact that exacerbate occurrences of hydrologic extremes. To investigate climate change impact on the future precipitation and temperature of NRB, a regional climate model, weather research and forecasting (WRF) was set up at one domain, 36-km resolution to dynamically downscale the base period (1976–2005), RCP4.5 and RCP8.5 climate scenarios of four General Circulation Model (GCMs) of CMIP5 over NRB for 2050s and 2080s. For base periods, WRF simulated surface temperature and precipitation that agree well with observed CRU and GPCC data of NRB, respectively. Under downscaled RCP4.5 and RCP8.5 climate scenarios, the annual precipitation of Blue Nile, Atbara, and Sobat river basin, Bahar El Ghazal and Lake Victoria regions are projected to change by about [− 7, 14.2], [− 19, 25.3], [− 7, 39], [− 5.9, 23], and [3.6, 27] % in the 2050s, and [− 14, 25], [− 22.5, 39], [− 4.7, 60.4], [− 11, 31], and [11.8, 41] % in the 2080s, respectively. The mean annual air temperature for sub-basins of NRB is projected to increase by 1.67–2 °C in the 2050s, 2–2.5 °C in the 2080s under RCP4.5, and by 2.5–3 °C in the 2050s and 3.9–4.6 °C in the 2080s under RCP8.5, respectively. Most precipitation extreme indices investigated are projected to increase, which implies that NRB could experience more severe and frequent extreme precipitation in future. Furthermore, extreme temperature indices of NRB are projected to decrease in cold, but increase in warm night/days.