COVID-19 presented countries with unprecedented health policy challenges. For low-income countries in particular, policymakers had to contend with both the direct threats posed by COVID-19 as well as the social, educational, and economic harms associated with lockdown and other infection prevention and control measures. We present a holistic and contextualised case study of the direct and indirect impacts of COVID-19 on women and children, with some assessment of their uneven distribution across socio-economic, age and gender groups. We used different types of primary and secondary data from multiple sources to produce a holistic descriptive analysis. Primary data included: qualitative data obtained from 28 in-depth interviews of key informants, six focus group discussions; and 40 household interviews. We also extracted data from government reports and announcements, the District Health Information Software version 2 (DHIS2), newspaper articles and social media, as well as from published research articles. Our findings show that the direct and indirect adverse impacts of COVID-19 were compounded by many years of severe political economic challenges, and consequent deterioration of the healthcare system. The indirect effects of the pandemic had the most severe impacts on the poorest segment of society and widened age and gender inequalities. The pandemic and its accompanying infection prevention and control measures negatively affected health service delivery and uptake. The management of COVID-19 presented enormous challenges to policymakers and public health specialists. These included managing the greatest tension between direct and indirect harms; short-term and long-term effects; and the unequal distribution of harms across different segments of society.