In today's highly competitive marketplace, supply chain (SC) and product development activities should be coordinated and synchronized so that market demand, product release and capacity requirements are matched in a financially sustainable fashion. In this work, an integrated model is developed which incorporates simultaneous treatment of SC design-planning and R&D decisions in the pharmaceutical industry. Moreover, the aforementioned cross-functional model embeds a capital budgeting formulation enabling the quantitative assessment of the firms’ value. The model also considers the endogenous uncertainty associated with product test outcomes during the development process. To tackle this problem, a scenario based multi-stage stochastic mixed integer linear programming (MILP) formulation is proposed. This model includes risk constraints which allow finding optimal solutions within accepted risk levels. A decomposition technique is applied in order to reduce the computational effort required for the solution of the monolithic model, thus facilitating the solution of realistic industrial problems of moderate scale.