Between September and December 2023, Uruguay experienced unusually high pinniped mortality due to an HPAI-H5N1 virus outbreak. We examined and compared the temporal distribution of strandings and swab results. Data on pinniped strandings was compiled from the Stranding Network project and governmental institutions, and the number of positive and total swabs conducted was obtained through government public information requests. A total of 2713 stranded pinnipeds were recorded; 92.4% were dead, including 80 aborted fetuses. Live stranded animals showed clinical signs such as tremors, convulsions, and extreme weakness. Strandings peaked from mid-September to early November. Species was identified in 1121 cases: 56.1% were South American sea lions (SASL), and 42.6% were South American fur seals (SAFS). Out of 159 swabs, 22.6% tested positive for HPAI-H5N1. Most positive cases were unidentified pinnipeds, 33% in SASL and 22% in SAFS. The estimated mortality reached 1465 SASL, about 15% of the population, significantly affecting the declining population and its reproductive stock. The outbreak response revealed weaknesses in disease surveillance, poor institutional coordination, and delayed swabbing efforts. Improved management strategies are necessary to protect vulnerable species from emerging diseases and catastrophic events.