Effects of change in weather conditions on the yields of Basmati 370 and IR 2793-80-1 cultivated under System of Rice Intensification (SRI) in Mwea and Western Kenya irrigation schemes were assessed through sensitivity analysis using the Ceres rice model v 4.5 of the DSSAT modeling system. Genetic coefficients were determined using 2010 experimental data. The model was validated using rice growth and development data during the 2011 cropping season. Two SRI farmers were selected randomly from each irrigation scheme and their farms were used as research fields. Daily maximum and minimum temperatures and precipitation were collected from the weather station in each of the irrigation schemes while daily solar radiation was generated using weatherman in the DSSAT shell. The study revealed that increase in both maximum and minimum temperatures affects Basmati 370 and IR 2793-80-1 grain yield under SRI. Increase in atmospheric CO2concentration led to an increase in grain yield for both Basmati and IR 2793-80-1 under SRI and increase in solar radiation also had an increasing impact on both Basmati 370 and IR 2793-80-1 grain yield. The results of the study therefore show that weather conditions in Kenya affect rice yield under SRI and should be taken into consideration to improve food security.