The Nile river basin is one of the global hotspots vulnerable to climate change impacts due to fast growing population and geopolitical tensions. Previous studies demonstrated that general circulation models (GCMs) frequently show disagreement in the sign of change in annual precipitation projections. Here, we first evaluate the performance of 20 GCMs from the 6 Coupled Model Intercomparison Project (CMIP6) benchmarked against a high spatial resolution precipitation dataset dating back to 1983 from Precipitation Estimation from Remotely Sensed Information using Artificial Neural Networks - Climate Data Record (PERSIANN-CDR). Next, a Bayesian Model Averaging (BMA) approach is adopted to derive probability distributions of precipitation projections in the Nile basin. Retrospective analysis reveals that most GCMs exhibit considerable (up to 64% of mean annual precipitation) and spatially heterogenous bias in simulating annual precipitation. Moreover, it is shown that all GCMs underestimate interannual variability; thus, the ensemble range is under-dispersive and a poor indicator of uncertainty. The projected changes from the BMA model show that the value and sign of change varies considerably across the Nile basin. Specifically, it is found that projected change in the two headwaters basins, namely Blue Nile and upper White Nile is 0.03% and -1.65% respectively; both statistically insignificant at 0.05. The uncertainty range estimated from the BMA model shows that the probability of a precipitation decrease is much higher in the upper White Nile basin whereas projected change in the Blue Nile is highly uncertain both in magnitude and sign of change.