There is substantial empirical evidence that input subsidy programs have a significant impact on agricultural productivity in Africa. However, the association between agro-ecological conditions and the magnitude of the impact of these public interventions remains unknown. This study takes into account differences in agro-ecological conditions to assess the impact of the fertiliser subsidy program on maize yield in Burkina Faso. By relying on an endogenous switching regression and using a nationally representative household data collected by the ministry of agriculture in 2012, we find that the fertiliser subsidy increases maize yield by about 222.82 kg/ha. Furthermore, the impact of the program is found to be largely higher in the Sudanian zone (267.88 kg/ha) than in the Sudano-Sahelian zone (151.00 kg/ha). To accelerate agricultural growth for poverty reduction in rural Burkina Faso, our findings suggest policy makers to adjust this policy regarding agro-ecological zones for more effectiveness.