The coronavirus pandemic (COVID-19) has triggered a public health and economic crisis in high and low resource settings since the beginning of 2020. With the first case being discovered on 12th March 2020, Kenya has responded by using health and non-health strategies to mitigate the direct and indirect impact of the disease on its population. However, this has had positive and negative implications for the country’s overall health system. This paper aimed to understand the pandemic’s impact and develop lessons for future response by identifying the key challenges and opportunities Kenya faced during the pandemic. We conducted a qualitative study with 15 key informants, purposefully sampled for in-depth interviews from September 2020 to February 2021. We conducted direct content analysis of the transcripts to understand the stakeholder’s views and perceptions of how COVID-19 has affected the Kenyan healthcare system. Most of the respondents noted that Kenya’s initial response was relatively good, especially in controlling the pandemic with the resources it had at the time. This included relaying information to citizens, creating technical working groups and fostering multisectoral collaboration. However, concerns were raised regarding service disruption and impact on reproductive health, HIV, TB, and non-communicable diseases services; poor coordination between the national and county governments; shortage of personal protective equipment and testing kits; and strain of human resources for health. Effective pandemic preparedness for future response calls for improved investments across the health system building blocks, including; human resources for health, financing, infrastructure, information, leadership, service delivery and medical products and technologies. These strategies will help build resilient health systems and improve self-reliance, especially for countries transitioning from donor aid such as Kenya in the event of a pandemic.