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To better understand the wide variation of performance among county health systems in Kenya, this study investigated their performance determinants. We selected five counties with varied performance and examined their performance across five domains containing 10 thematic areas. We conducted a stakeholder analysis, consisting of focus group discussions and key informant interviews, and administered a quantitative survey to quantify the magnitude of inefficiency. The study found that a shortage of funding was one of the most common complaints from counties, leading to inefficiency in the health system. Another major reason for inefficiencies was the delay in disbursing funding to health facilities, which affected the procurement of medical supplies and commodities essential for delivering healthcare to the population. In addition, lack of autonomy in procuring commodities and equipment was repeatedly mentioned as a barrier to delivering quality health services. Other reported common concerns contributing to the performance of county health systems were the lack of lab tests and equipment, low willingness to join health insurance, rigid procurement policies and lengthy procurement process, lack of motivation and incentives for service delivery, and poor economic status. Despite the common concerns among the five counties, they differed in some schematic areas, such as the county's commitment to health and community mobilization. In summary, this study suggests various factors that determine county health system performance. Given the multifaceted nature of inefficiency drivers, it is necessary to adopt a holistic approach to address the causes of inefficiencies and improve the county health systems., (© The Author(s) 2021. Published by Oxford University Press in association with The London School of Hygiene and Tropical Medicine. All rights reserved. For permissions, please e-mail: journals.permissions@oup.com.)