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In the wake of a rapidly changing climate, droughts have intensified, in both duration and severity, across the globe. The Germanwatch long-term Climate Risk Index ranks Pakistan among the top 10 countries most affected by the adverse effects of climate change. Within Pakistan, the province of Balochistan is among the most vulnerable regions due to recurring prolonged droughts, erratic precipitation patterns, and dependence on agriculture and livestock for survival. This study aims to explore how the characteristics of droughts have evolved in the region from 1902–2015 using 3-month and 12-month timescales of a popular drought index, the Standardized Precipitation Evapotranspiration Index (SPEI). The region was divided into six zones using Spatial “K”luster Analysis using Tree Edge Removal (SKATER) method, and run theory was applied to characterize droughts in terms of duration, severity, intensity, and peak. The results of the non-parametric Mann–Kendall trend test applied to SPEI indicate prevailing significant negative trends (dryer conditions) in all the zones. Balochistan experienced its most severe droughts in the 1960s and around 2000. The effects of climate change are also evident in the fact that all the long duration droughts occurred after 1960. Moreover, the number of droughts identified by 3-month SPEI showed a significant increase after 1960 for all six zones. The same trend was found in the 12-month SPEI but for only three zones.