Start-up companies play an important role in innovation and many of them have become the leaders of their fields. With limited capital and human resources, start-up companies face a range of challenges in managing their research and development (R&D) projects. This presentation covers three topics in relation to R&D project management. First, we consider how to design appropriate project selection standard in a principal -agent model where the agent prefers to maximize the subsidiary profit but the headquarters prefers to maximize the consolidate profit. An important result is that certain threshold policy (such as imposing a threshold on the consolidated profit) can be even worse than the naïve policy that does not impose any threshold. Second, we consider how to design time-based incentives to reward the agent’s effort on reducing the project completion time. We find that the performance of the fixed-payment-fixed-time (FPFT) contract and the linear-bonus contract critically depends on whether the time reduction is additive or multiplicative. When the time reduction is multiplicative, FPFT contract is much better than the linear-bonus contract; when the time reduction is additive, the opposite happens. Third, we consider how to design equity-based incentives under the concurrent and the sequential development strategies. The conventional wisdom suggests that compared with the concurrent development strategy, the sequential development strategy incurs a weakly lower cost but takes a longer time to complete a multi-task project. By contrast, we find that when the principal hires only one agent to perform all of the tasks and the agent’s effort is unobservable, the sequential development strategy could result in a higher agency cost. The single agent may under-exert effort in the early task but over-exert effort in the later task. In a wide range of parameter space, the concurrent development strategy not only reduces the principal’s cost but also reduces the completion time.