The termination of the Holocene African Humid Period (~9 to ~6 kyr BP) is simulated with a three-dimensional global coupled climate model that resolves synoptic variability associated with weather patterns. In the simulation, the potential for green and desert Sahara states becomes equal between 7.5 and 5.5 thousand years ago, causing the climate system to fluctuate between these states at decadal-to-centennial time-scales. This model result is supported by paleoevidence from the Western Sahara region, showing similar paleohydrological fluctuations around that time. For the present-day, only the desert Sahara state is stable in the model.