The study aims to analyze climate variability and farmers’ perception in Southern Ethiopia. Gridded annual temperature and precipitation data were obtained from the National Meteorological Agency (NMA) of Ethiopia for the period between 1983 and 2014. Using a multistage sampling technique, 403 farm households were surveyed to substantiate farmers’ perceptions about climate variability and change. The study applied a nonparametric Sen’s slope estimator and Mann–Kendall’s trend tests to detect the magnitude and statistical significance of climate variability and binary logit regression model to find factors influencing farm households’ perceptions about climate variability over three agroecological zones (AEZs). The trend analysis reveals that positive trends were observed in the annual maximum temperature, 0.02°C/year () in the lowland and 0.04°C/year () in the highland AEZs. The positive trend in annual minimum temperature was consistent in all AEZs and significant (). An upward trend in the annual total rainfall (10 mm/year) () was recorded in the midland AEZ. Over 60% of farmers have perceived increasing temperature and decreasing rainfall in all AEZs. However, farmers’ perception about rainfall in the midland AEZ contradicts with meteorological analysis. Results from the binary logit model inform that farmers’ climate change perceptions are significantly influenced by their access to climate and market information, agroecology, education, agricultural input, and village market distance. Based on these results, it is recommended to enhance farm households’ capacity by providing timely weather and climate information along with institutional actions such as agricultural extension services.