Medical waste management is crucial in densely populated urban areas of developing nations. The disposal of biohazardous medical waste requires strict monitoring due to potential environmental and public health risks. In developing countries, several constraints present as challenges to medical waste disposal, including inaccessible biohazardous disposal plants, limited in-facility biohazardous waste storage, government regulation, and cost. Surabaya, Indonesia’s second-largest city, experiences these challenges. Currently, the Surabaya Health Department (SHD) relies on third-party waste processing vendors to handle infectious waste from 63 health facilities due to hazardous waste disposal only being permitted at the provincial level. In addition, waste collection occurs monthly for most health facilities, with a regulated 14-day storage period to prevent accumulation which contradicts the minimum 25-kg threshold that third-party vendors implement. This study utilizes Surabaya’s context to develop an effective medical waste disposal and transportation strategy and logistics using the Periodic Vehicle Routing Problem (PVRP). Results indicate that the 14-day storage requirement benefits SHD and vendors, improving operational efficiency and mitigating risks. Compliance with storage regulations reduces travel distances compared to scenarios without storage requirements. This study’s methodology applies to developing countries exhibiting similar constraints and acts as a guideline to develop similar medical waste disposal strategies.