In this paper, the relationship between climate variation and crop output in Uganda for the period 1981 to 2008 is examined. The time-varying ARCH model of the crop production function is used to estimate the relationships. Analysis of the incidence of rainfall and temperature variation from the long-term average indicates that it is insignificant. Estimates of the trend of rainfall and temperature suggest a gradual decline in volume of rainfall and record of temperatures in Uganda in the present and near future. ARCH model estimates show that a variation in rainfall and temperature from the long-term mean has significant effects on crop output, while exponential increase in rainfall has detrimental effect on crop output. It is recommended that the government should support farmers to adopt small-scale irrigation systems; and capacity of weather forecast agencies should be strengthened to monitor and educate the public on present and potential near-future climate variations.