The paper focused on the assessment of secondary healthcare administration in Lagos with respect to examined the administrative structure put in place in secondary healthcare facilities and evaluated the effects of administrative structure on secondary healthcare service in Lagos as well as analysed the challenges confronting the administration of secondary healthcare service in Lagos. The paper employed descriptive research design and quantitative research approach. The data were gathered through administration of structured questionnaire. The paper used 20% of the study population 1341, making 268 sample size for questionnaire which consisted of both medical and non-medical staff of three selected General Hospital in Lagos i.e. one from each senatorial district in Lagos State. Data collected were analysed using frequency distribution, percentages, tables, and t-test. The study revealed that sustainability of administrative structure put in place in Lagos State to manage the secondary healthcare service are impactful and has significant effects on the services rendered. Therefore, the paper recommended that hospital administration should provide up to date medical technology and infrastructure need to easy the work of health workers and promote service delivery and that government should be an increase in the financial commitment and budget allocation of the government to the health care sector to address the existing financial challenges. The paper concluded that sustainability of administrative structure has direct effect on secondary healthcare on service delivery in Lagos, Nigeria. 
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