In 2015, South Africa experienced one of the worst (El Niño-induced) droughts in 35 years. This affected economic activities, individual and community livelihoods and wellbeing especially in rural communities in northern KwaZulu-Natal. Drought’s direct and indirect impacts on public health require urgent institutional responses, especially in South Africa’s stride to eliminate HIV as a public health threat by 2030 in line with the UNAIDS goals. This paper draws on qualitative data from interviews and policy documents to discuss how the devastating effect of the 2015 drought experience in the rural Hlabisa sub-district of uMkhanyakude, a high HIV prevalence area, imposes an imperative for more proactive institutional responses to drought and other climate-related events capable of derailing progress made in South Africa’s HIV/AIDS response. We found that drought had a negative impact on individual and community livelihoods and made it more difficult for people living with HIV to consistently engage with care due to economic losses from deaths of livestock, crop failure, food insecurity, time spent in search of appropriate water sources and forced relocations. It also affected government institutions and their interventions. Interviewed participants’ reflections on drought-related challenges, especially those related to institutional and coordination challenges, showed that although current policy frameworks are robust, their implementation has been stalled due to complex reporting systems, and inadequate interdepartmental collaboration and information sharing. We thus argue that to address the gaps in the institutional responses, there is a need for more inclusive systems of drought-relief implementation, in which government departments, especially at the provincial and district levels, work with national institutions to better share data/information about drought-risks in order to improve preparedness and implementation of effective mitigation measures.