Food security in many countries is threatened due to rapid population growth. Rising temperatures and carbon dioxide, rainfall irregularity, and global warming may have serious consequences on rice production and hence food security. However, there is limited knowledge on the precise effects of global warming on crops, in particular on rice which is a major staple crop and contributor to food security. Most reports have focused on irrigated rice in India or China but much less is known about rainfed rice cropping systems in Madagascar. In the Malagasy highlands, the most populated part of Madagascar, land pressure has led to saturation of irrigated lands and the adoption of rainfed cropping systems on hilltops. The present article reports the impact of various climate changes on rice productivity in four cropping systems using the CERES-Rice model. The cropping systems include two tillages components, hand-plowed and no-tillage, and two fertilization rates: low and high nitrogen. A locally adapted rice cultivar was calibrated and validated using a dataset based on experiments conducted over a 6-year period. Daily weather data were generated for a set of 90 virtual years, from 2010 to 2099. Our results show that no-tillage systems have no advantage for climate change issues. Nitrogen was a major constraint for crops in hand-plowed and no-tillage systems. We found negative effects of climate change on soil carbon and nitrogen. By contrast, we found positive effects of temperature and increased CO2 on rice growth. The overall effects on rice yields are positive under the most pessimistic climate change scenarios but we demonstrate that the sustainability of these systems is threatened.