Biodiesel is a clean-burning alternative fuel, produced from domestic, renewable resources. It is biodegradable, nontoxic, and essentially free of sulfur and aromatics. Biodiesel is usually blended with hydro-carbon diesel with ratios 10-90 (called B-10) or 20-80 (called B-20). This bio mix is a tested model in various countries for use as alternative fuel. Biodiesel can be produced from a number of seed oils (used and unused). The production process for resources vary from one to another in terms of minor operational deviations. The flow line from stakeholder to consumer consists of the growing of seeds, oil extraction, chemical treatments, and consumption. This flow line involves a number of characters that can play their specific roles behind the scenes. This article proposes a strategy for the development of a supply-chain mechanism for the use of biodiesel as an alternative fuel in Pakistan. The rational of this article is an introduction of biodiesel including its viable sources in Pakistan and its subsequent benefits as principle motivators for the production of biodiesel in Pakistan and the worldwide development in this field. The actual theme of this article is supply-chain development strategy in Pakistan, which covers demand management, identification of inventory requirements, devising the production process flow, deployment models and basic infrastructure requirements. The attributes covered are the availability of raw materials, production processes, handling, transportation, distribution and storage in different stages. In the end, the authors have described expected challenges and uncertainties in deploying the supply chain of biodiesel as an alternate fuel in Pakistan and the possible solutions.