Community drug distributors (CDDs) who are volunteers have the responsibility of awareness creation, household census, drug distribution and record-keeping and are thus key stakeholders in the campaign for Lymphatic Filariasis (LF) elimination. Taking into account their experiences and perceptions is important for a successful elimination campaign. We conducted a qualitative study in 2018 to identify implementation challenges and opportunities for improved mass drug administration (MDA) uptake based on the CDDs perceptions and experiences. Within a larger study that used mixed methods quasi-experimental design, we collected qualitative data from two wards in Kaloleni Sub-County of Kilifi County which was purposively selected owing to its low, 56% and 50.5% treatment coverage in 2015 and 2016 respectively. Focus group discussions (FGDs) (n = 8) and in-depth interviews (IDIs) (n = 8) with CDDs, IDIs (n = 22) with opinion leaders and IDIs (n = 8) with health workers were conducted and the data analyzed by QSR NVIVO version 10 according to thematic areas. The results showed that based on the perceptions and experiences of the CDDs, several challenges: communities' refusal to take the drugs; absenteeism during MDA; non-adherence to CDDs selection criteria; inadequacy in number of CDDs engaged during the campaign and training provided; insufficiency of drugs issued to CDDs; lack of CDDs supervision and low motivation negatively impact on MDA uptake. Opportunities to address the challenges included: awareness creation on MDA, health education on LF and observation of hygiene during drug administration, increased duration of awareness creation and drug administration, adherence to CDDs selection criteria and putting into consideration the vastness of an area and population density while deploying CDDs. Other opportunities include: improved CDDs training and scheduling; issuing of enough drugs to CDDs to meet the communities' demand and improved supervision and motivation of CDDs. Addressing the challenges highlighted is an important step of maximizing MDA uptake. The opportunities presented need to be considered by the NTD program personnel, the county health personnel and the community while planning the implementation of MDA campaigns.