The objective of this study is to analyse the impact of COVID-19 measures on the health sector. We have investigated the level of preparedness of Kenya’s health system for COVID-19 pandemic using selected indicators of preparedness, analyzed the level of selected health indicators before COVID-19 pandemic and the impact of COVID-19 measures on these indicators. This study uses secondary data complemented with primary data to meet these objectives. Primary data were collected from an electronic questionnaire which returned a sample of 61 respondents from Machakos, Murang’a, Nyeri, Vihiga, Narok, Nakuru, Kiambu, Nyandarua and Embu. Information was also collected from Focus Group Discussions (FGDs) drawn from Kawangware, Kibra and Mathare informal settlements in Nairobi, Kenya. Key informants who were mainly health sector policy makers provided critical information regarding the impact of COVID-19 measures.