BackgroundThe WHO Non-Communicable Diseases Kit (NCDK) was developed to support care for non-communicable diseases (NCDs) in humanitarian settings. Targeting primary healthcare, each kit contains medicines and supplies that are forecasted to meet the needs of 10,000 people for 3 months. This study aimed to evaluate the NCDK deployment process, contents, usage and limitations, and to explore its acceptability and effectiveness among healthcare workers (HCWs) in South Sudan.MethodsThis mixed-method observational study captured data from pre-and-post NCDK deployment. Six data collection tools included: (i) contextual analysis, (ii) semi-structured interviews, in addition to surveys measuring/assessing (iii) healthcare workers’ knowledge about NCDs, and healthcare workers’ perceptions of: (iv) health facility infrastructure, (v) pharmaceutical supply chain, and (vi) NCDK content. The pre- and post-deployment evaluations were conducted in four facilities (October-2019) and three facilities (April-2021), respectively. Descriptive statistics were used for quantitative data and content analysis for open-ended questions. A thematic analysis was applied on interviews findings and further categorized into four predetermined themes.ResultsCompared to baseline, two of the re-assessed facilities had improved service availability for NCDs. Respondents described NCDs as a growing problem that is not addressed at a national level. After deployment, the same struggles were intensified with the COVID-19 pandemic. The delivery process was slow and faced delays associated with several barriers. After deployment, poor communications and the “push system” of inventories were commonly perceived by stakeholders, leading to expiry/disposal of some contents. Despite being out-of-stock at baseline, at least 55% of medicines were found to be unused post-deployment and the knowledge surveys demonstrated a need for improving HCWs knowledge of NCDs.ConclusionsThis assessment further confirmed the NCDK role in maintaining continuity of care on a short-term period. However, its effectiveness was dependent on the health system supply chain in place and the capacity of facilities to manage and treat NCDs. Availability of medicines from alternative sources made some of the NCDK medicines redundant or unnecessary for some health facilities. Several learnings were identified in this assessment, highlighting barriers that contributed to the kit underutilization.Supplementary InformationThe online version contains supplementary material available at 10.1186/s13031-023-00525-w.