In the fight against infectious diseases, social inequalities in health (SIH) are generally forgotten. Mali, already weakened by security and political unrest, has not been spared by the COVID-19 pandemic. Although the country was unprepared, the authorities were quick to implement public health measures, including a SARS-CoV-2 testing program. This study aimed to understand if and how social inequalities in health were addressed in the design and planning for the national COVID-19 testing policy in Mali. A qualitative survey was conducted between March and April 2021 in Bamako, the capital of Mali. Twenty-six interviews were conducted with key government actors and national and international partners. A document review of national reports and policy documents complemented this data collection. The results demonstrated that the concept of SIH was unclear for the participants and was not a priority. The authorities focused on a symptom-based testing strategy that was publicly available. Participants also mentioned some efforts to reduce inequalities across geographical territories. The reflection and consideration of SIH within COVID-19 interventions was difficult given the governance approach to response efforts. The urgency of the situation, the perceptions of COVID-19, and the country’s pre-existing fragility were factors limiting this reflection. Over time, little action has been taken to adapt to the specific needs of certain groups in the Malian population. This study (re)highlights the need to consider SIH in the planning stages of a public health intervention to adapt its implementation and to limit the negative impact on SIH.