This study investigated the trends and variability of seasonal and annual rainfall and temperature data over southern Ethiopia using time series analysis for the period 1983–2016. Standard Anomaly Index (SAI), Coefficient of Variation (CV), Precipitations Concentration Index (PCI), and Standard Precipitation Index (SPI) were used to examine rainfall variability and develop drought indices over southern Ethiopia. Temporal changes of rainfall trends over the study period were detected using Mann Kendall (MK) trend test and Sen’s slope estimator. The results showed that the region experienced considerable rainfall variability and change that resulted in extended periods of drought and flood events within the study period. Results from SAI and SPI indicated an inter-annual rainfall variability with the proportions of years with below and above normal rainfall being estimated at 56% and 44% respectively. Results from the Mann Kendall trend test indicated an increasing trend of annual rainfall, Kiremt (summer) and Bega (dry) seasons whereas the Belg (spring) season rainfall showed a significant decreasing trend (p < 0.05). The annual rate of change for mean, maximum and minimum temperatures was found to be 0.042 °C, 0.027 °C, and 0.056 °C respectively. The findings from this study can be used by decision-makers in taking appropriate measures and interventions to avert the risks posed by changes in rainfall and temperature variability including extremes in order to enhance community adaptation and mitigation strategies in southern Ethiopia.