Variations in agricultural production due to rainfall and temperature fluctuations are a primary cause of food insecurity on the African continent. Analysis of changes in phenology can provide quantitative information on the effect of climate variability on growing seasons in agricultural regions. Using a robust statistical methodology, we describe the relationship between phenology metrics derived from the 26 year AVHRR NDVI record and the North Atlantic Oscillation index (NAO), the Indian Ocean Dipole (IOD), the Pacific Decadal Oscillation (PDO), and the Multivariate ENSO Index (MEI). We map the most significant positive and negative correlation for the four climate indices in Eastern, Western and Southern Africa between two phenological metrics and the climate indices. Our objective is to provide evidence of whether climate variability captured in the four indices has had a significant impact on the vegetative productivity of Africa during the past quarter century. We found that the start of season and cumulative NDVI were significantly affected by large scale variations in climate. The particular climate index and the timing showing highest correlation depended heavily on the region examined. In Western Africa the cumulative NDVI correlates with PDO in September–November. In Eastern Africa the start of the June–October season strongly correlates with PDO in March–May, while the PDO in December–February correlates with the start of the February–June season. The cumulative NDVI over this last season relates to the MEI of March–May. For Southern Africa, high correlations exist between SOS and NAO of September–November, and cumulative NDVI and MEI of March–May. The research shows that climate indices can be used to anticipate late start and variable vigor in the growing season of sensitive agricultural regions in Africa.