The research examined effect of climate variability on yield of the two dominant cool weather cereals (wheat and barley) in central highland and Arssi grain plough farming systems of Ethiopia using eight round unbalanced panel data (1994-2014). The stochastic frontier model result revealed that production inputs for producing wheat and barley in the two farming system had significant effect. Crop season rainfall increment had negative and significant effect on technical efficiency of smallholders to produce wheat as to the model result. Technical efficiency of two crops responded differently for cropping season rainfall variability, in which wheat had negative and significant interaction with it while barley had positive. Given this, cropping season temperature had significant and positive effect on technical efficiency of both wheat and barley. Having this into account, yield of the two crops responded similarly for changes in production inputs like working capital, human labor and fertilizer. In general, rainfall inconsistency at the different stages of the production period had strong effect on yield of the two crops. Given this, the study forwarded an assignment to plant scientists in order to have further investigation on how the two crops responded differently to temperature variability.