An innovative R&D project that creates a great business opportunity usually involves high technological and market uncertainty. It is easy to see that developing only one solution approach in the R&D project is too risky. The selectionism or the parallel development strategy can be applied to construct an innovation funnel that increases the flexibility to hedge against the uncertainty. However, little research has been devoted to selection of which alternative solution approaches should be included for the innovation funnel. This research aims to develop a simulation‐based methodology that can help R&D managers evaluate and construct an innovation funnel containing promising alternative approaches for a novel R&D project to maximize project profit, while minimizing downside risk within an allowable loss. A new risk measure based on the concept of conditional value‐at‐risk from the finance literature is defined to evaluate the project downside risk. An example of drug development project is used to illustrate the proposed methodology. We recommend that firms should improve their capabilities on market research, concept screening, and R&D efficiency for taking full advantages of selectionism.