Savannas cover large areas of the Earth's surface and play an important role in global carbon cycling. West Africa is dominated by a variety of savanna ecosystems; however, they have been poorly studied up to now. In the present study, energy and carbon dioxide exchange was measured over a 2-year period using the eddy covariance technique at a southern Sudanian savanna site in Burkina Faso that was not subject to human disturbances except for annual burning. Turbulent energy exchange was dominated by sensible heat flux in the dry season (November–May) and by latent heat flux in the wet season (June–September), with peak values higher than 300 W m⁻² and lower than 100 W m⁻² for the dominating and the minor component, respectively. The ecosystem was a marginal CO₂ source in the dry season, whereas significant CO₂ uptake was found in the rainy season. CO₂ fluxes showed a clear diurnal pattern, with mean release rates of 0.2 mg CO₂ m⁻² s⁻¹ during nighttime and mean maximum uptake rates of 1.0 mg CO₂ m⁻² s⁻¹ in July and August around midday. Diurnal courses of CO₂ flux were in phase with photosynthetically active radiation (PAR). Highest CO₂ uptake rates of more than 0.8 mg CO₂ m⁻² s⁻¹ occurred at PAR levels in excess of 1000 μmol m⁻² s⁻¹. Total net ecosystem CO₂ uptake was 179 ± 98 g C m⁻² in the first year and 429 ± 100 g C m⁻² in the second year of investigation, including an estimate of annual fire C loss of 149 g C m⁻². The remarkable difference in net CO₂ uptake between the two years could be explained by higher rainfall in 2006, revealing the sensitivity of the ecosystem to water availability and rainfall distribution that could lead to a significant change in C sequestration patterns under a changing climate.