Understanding how climate change might impact agricultural systems at a household level is crucial in the development of adaptation strategies. In this study we assessed the sensitivity of four different types of smallholder mixed crop-livestock systems in Burkina Faso, to the potential impacts of climate change, based on the changes in household income and kilocalorie production. The four systems with different levels of resource endowment were simulated over 99 years using a whole farm model (APSFarm-LivSim), under current and future climate. The climate data for current climate variability and the climate change scenario were generated using the MarkSim™ tool. For future scenarios, we used the ensemble means of 17 global circulation models (CMIP5 data) for 2050, and IPCC scenario RCP 8.5. Under the projected climate scenario, average annual rainfall is expected to increase from 607mm to 674 mm (+11%). Additionally, average temperature is likely to increase by 2.6°C. Overall, these changes in climate showed to negatively affect crop yields, particularly cowpea (-25%), millet (-15%) and groundnuts (-5%); while sorghum and maize did not show significant changes in yields. At the household level, income and kilocalorie production were reduced by up to 17% and 13%, respectively, in a market-oriented household with a relatively smaller area per capita. Furthermore, we introduced two levels of fertilization in the simulation (+30 +60 Kg/N/Ha). The simulation showed that fertilizers have a positive impact on yields under current climate; however this effect decreases under the climate change scenario. For example, when adding 60 Kg/N/Ha, average maize yields increased by 145% under the current climate scenario, but only by 105% under the projected climate change scenario. This suggests that climate change might limit the potential of the farms to increase productivity.