Based on a 3-year period of infrared scintillometry, soil and meteorological measurements, this study presents an analysis of the surface energy balance partitioning over a heterogeneous savannah, in the Sudano-Sahelian region. The site is located in Northern Benin, meso-site of the African Monsoon Multidisciplinary Analyses (AMMA) project. The 3-year period enables an analysis of several alternate dry and wet periods, as well as the intermediate dry-to-wet and wet-to-dry periods. Infrared scintillometry, coupled with measurements of the available energy (net radiation minus ground heat flux) and a careful analysis of the aerodynamic properties of the scintillometer footprint, are employed to provide robust estimates of the turbulent (sensible and latent heat) fluxes over complex terrain, in terms of the topography and in terms of the spatially and temporally heterogeneous vegetation cover. A characterization of the uncertainties on each term of the energy balance is given at the scale of the scintillometer footprint. These uncertainties strongly depend on the season for the residual latent heat flux. Results point out that the climate of the Sudano-Sahelian region is characterized by a strong seasonal cycle and inter-annual variability, related to changing atmospheric and land surface conditions. The evaporative fraction is found to be relatively constant during the wet period (0.67) and more variable during the dry and intermediate periods. In addition, sensible heat flux and net radiation are well correlated during the dry season. The diurnal cycle shows a predominance of evaporation during the wet season and sensible heat during the dry season. Results point a significant latent heat flux during the dry period, signature of persistent vegetation in the Sudano-Sahelian region. Finally, that data set at hourly time step would provide useful information for modelling and the parameterization of the associated processes for this region.