As human immunodeficiency virus (HIV) treatment programs expand in Africa, delivery systems must be strengthened to support patient retention. Clinic characteristics may affect retention, but a relationship between clinic flow and attrition is not established. This project characterized HIV patient experience and flow in an urban Kenyan clinic to understand how these may affect retention. We used Toyota’s lean manufacturing principles to guide data collection and analysis. Clinic flow was evaluated using value stream mapping and time and motion techniques. Clinic register data were analyzed. Two focus group discussions were held to characterize HIV patient experience. Results were shared with clinic staff. Wait times in the clinic were highly variable. We identified four main barriers to patient flow: inconsistent patient arrivals, inconsistent staffing, filing system defects, and serving patients out of order. Focus group participants explained how clinic operations affected their ability to engage in care. Clinic staff were eager to discuss the problems identified and identified numerous low-cost potential solutions. Lean manufacturing methodologies can guide efficiency interventions in low-resource healthcare settings. Using lean techniques, we identified bottlenecks to clinic flow and low-cost solutions to improve wait times. Improving flow may result in increased patient satisfaction and retention.