Interannual variability of African rainfall impacts local and global communities, but its past behavior and response in future climate projections are poorly understood. This is primarily due to short instrumental records and a lack of long high-resolution palaeoclimate proxy records. Here we present an annually resolved 91,000 year Early Pleistocene record of hydroclimate from the early hominin-bearing Makapansgat Valley, South Africa. Changes in speleothem annual band thickness are dominated by precession over four consecutive orbital cycles with strong millennial-scale periodicity. The frequency of interannual variability (2.0–6.5 yr oscillations) does not change systematically, yet its amplitude is modulated by the orbital forcing. These long-term characteristics of interannual variability are reproduced with transient climate model simulations of water balance for South Africa from the Late Pleistocene to Recent. Based on these results, we suggest that the frequency of interannual variations in southern African rainfall is likely to be stable under anthropogenic warming, but that the size of year-to-year variations may increase. We see an orbitally forced increase in the amplitude of interannual climate variability between 1.8 Ma and 1.7 Ma coincident with the first evidence for the Acheulean stone tool technology.