To deal with COVID-19, vaccination is a strategy adopted by many countries including the Democratic Republic of the Congo (DRC). The first phase of vaccination was conducted in 2021 as part of the country's Expanded Program on Immunization (EPI). To evaluate it, an intra-action review was conducted. It identified a low proportion of vaccinated vulnerable populations, namely health professionals (1.8%), chronically ill (0.09%), and older adults aged ≥ 55 (0.4%). The objective was to explore perceptions and barriers to acceptance of the COVID-19 vaccine in the DRC among the vulnerable populations targeted by the EPI. A qualitative study was conducted between September 2021 and June 2022 in Kinshasa, DRC. Semi-structured focus groups were conducted with each group separately using a single interview guide. It included five categories: socio-demographic information, COVID-19 vaccine status, perceptions towards the COVID-19 vaccination, vaccine hesitancy and perceptions towards the COVID-19 vaccination campaign. Three focus groups were conducted. In total, we had 16 participants with eight health professionals, four chronically ill participants, and four older adults. The majority were married (68.7%) and came from urban areas (68.7%). The sex ratio was at 1 and more than one-third had an education level equivalent to a master's degree (37.5%). Half were vaccinated against the COVID-19 (50.0%). The main perceptions and hesitancy factors were the lack of trust and knowledge of the vaccine's properties, benefits, and risks. Adjustment of the information messages which, according to participants, were not clear and poorly adapted to the needs of each group is the main element to improve the vaccination campaign. This study represents an important step to improve the COVID-19 vaccination campaign in the DRC. It showed the different barriers to the COVID-19 vaccines acceptance among vulnerable populations.