The headwater region of the upper Blue Nile is the main source of the Nile water for the three Eastern Nile countries, namely Ethiopia, Sudan, and Egypt. Climate-related studies for the region is thus paramount. However, previous studies for the region used non-homogenous data, and did not remove all the significant autocorrelations in trend analysis. Therefore, this study analyzed the trend using gap-filled and homogenized meteorological data over the period 1980 − 2017. Using the non-parametric Mann–Kendall test adjusted by effective sample size, the influence of all significant positive and negative autocorrelations on the trend was removed. Sen’s slope was used to determine the magnitude of trends. The tests were applied to minimum and maximum temperatures, mean temperature, diurnal temperature range (DTR), and total precipitation as well as seasonal and annual extreme climate indices. In general, the climate in the study region has become wetter and warmer. As for extreme temperature, the hot ends of the daily temperature distribution have altered more rapidly than the cold ends. Accordingly, the DTR exhibited a consistent increasing trend across the stations. The rainfall showed increases in maximum 1 − day precipitation amount, maximum 5 − day precipitation amount, number of heavy precipitation days, total annual rainfall, and extremely wet days. As trend magnitudes of the homogenized series differed from those of the original series, the results that emerged from the previous hydroclimate-related studies for the region using non-homogenized data should be revised. This study has significant implications for water use efficiency and adaptation to climate risk in the three riparian countries, given the recently commenced water resources projects.