Efficiency gains is a potential strategy to expand Kenya's fiscal space for health. We explored health sector stakeholders' understanding of efficiency and their perceptions of the factors that influence the efficiency of county health systems in Kenya. We conducted a qualitative cross-sectional study and collected data using three focus group discussions during a stakeholder engagement workshop. Workshop participants included health sector stakeholders from the national ministry of health and 10 (out 47) county health departments, and non-state actors in Kenya. A total of 25 health sector stakeholders participated. We analysed data using a thematic approach. Health sector stakeholders indicated the need for the outputs and outcomes of a health system to be aligned to community health needs. They felt that both hardware aspects of the system (such as the financial resources, infrastructure, human resources for health) and software aspects of the system (such as health sector policies, public finance management systems, actor relationships) should be considered as inputs in the analysis of county health system efficiency. They also felt that while traditional indicators of health system performance such as intervention coverage or outcomes for infectious diseases, and reproductive, maternal, neonatal and child health are still relevant, emerging epidemiological trends such as an increase in the burden of non-communicable diseases should also be considered. The stakeholders identified public finance management, human resources for health, political interests, corruption, management capacity, and poor coordination as factors that influence the efficiency of county health systems. An in-depth examination of the factors that influence the efficiency of county health systems could illuminate potential policy levers for generating efficiency gains. Mixed methods approaches could facilitate the study of both hardware and software factors that are considered inputs, outputs or factors that influence health system efficiency. County health system efficiency in Kenya could be enhanced by improving the timeliness of financial flows to counties and health facilities, giving health facilities financial autonomy, improving the number, skill mix, and motivation of healthcare staff, managing political interests, enhancing anticorruption strategies, strengthening management capacity and coordination in the health sector.