Running buffalo clover (Trifolium stoloniferum) is a federally endangered plant that was historically abundant and widespread from Kansas to West Virginia. Here we describe population trends and patch-scale population characteristics of T. stoloniferum based on more than two decades of sampling at the Blue Grass Army Depot in central Kentucky, the site with the most patches of this species across its extant range. A total of 168 patches of T. stoloniferum have been discovered at the site since 1992. Beginning in 2001, we conducted counts of individual ramets and inflorescences in each patch, and observed a range of 1160–9574 ramets and 54–2054 inflorescences per year from 2001 to 2014. While the number of individual ramets and inflorescences fluctuated widely among years, patches have steadily disappeared. Of all patches known since 1992, 66% are extirpated. The size of a T. stoloniferum patch is strongly related to its probability of persistence: patches with 20 or fewer ramets had a 50% chance of disappearing over a ten year period. Population viability analysis suggests <75% probability of extinction for 9 of 11 US Fish and Wildlife Service designated populations, but confidence intervals for 5 out of 11 populations include a 95% chance of extinction within 20 years. These findings highlight the importance of conducting more intensive population studies and developing better management strategies.