<p>Climate change poses significant challenges to rain-fed agriculture in Ethiopia, particularly in the northeastern highlands, where smallholder farmers are highly vulnerable to rainfall variability and temperature extremes. This study analyzes spatiotemporal trends in rainfall and temperature (1988–2020) and their impacts on rain-fed crop production in Wollo and the Oromia Special Zone of northeastern Ethiopia. Trends were analyzed using the Mann–Kendall test and Sen’s slope estimator. Rainfall variability was evaluated using the Coefficient of Variation (CV), Precipitation Concentration Index (PCI), and Rainfall Anomaly Index (RAI). Climate variability impacts on crop yields were assessed through correlation and regression analyses. Rainfall showed considerable spatial and seasonal variability, with the highest interannual variability observed during the small and dry seasons. The anomalies indicated interannual and seasonal variability, with frequent years experiencing below-average rainfall than above-normal rainfall. The Mann–Kendall test revealed non-significant decreasing trends in annual and seasonal rainfall at most stations, except at Kobo and Alamata, which showed statistically significant downward trends likely due to recurrent droughts and their lowland exposure. Across all stations and seasons, warming trends were observed, both maximum and temperatures. Correlation analysis revealed that most crop yields are positively correlated with rainfall but negatively associated with temperatures. The interannual variability in yield reflects a strong climate influence, resulting in declining yields for tef, wheat, and barley, while sorghum appears to be better adapted to changing climatic conditions. Therefore, tailored local adaptation strategies and context-specific planning could be essential for developing a climate-resilient agriculture system in the study region.</p>