Variability analyses for the rainfall over the Nile Basin have been confined mostly to sub-basins and the annual mean of the hydroclimatic variable based on observed short-term data from a few meteorological stations. In this paper, long-term country-wide rainfall over the period 1901–2011 was used to assess variability in the seasonal and annual rainfall volumes in all the River Nile countries in Africa. Temporal variability was determined through temporal aggregation of series rescaled nonparametrically in terms of the difference between the exceedance and non-exceedance counts of data points such that the long-term average (taken as the reference) was zero. The co-occurrence of the variability of rainfall with those of the large-scale ocean–atmosphere interactions was analyzed. Between 2000 and 2012, while the rainfall in the equatorial region was increasing, that for the countries in the northern part of the River Nile was below the reference. Generally, the variability in the rainfall of the countries in the equatorial (northern) part of the River Nile was found to be significantly linked to occurrences in the Indian and Atlantic (Pacific and Atlantic) Oceans. Significant linkages to Niño 4 regarding the variability of both the seasonal and annual rainfall of some countries were also evident.