Climate change and sea-level rise (SLR) are expected to increase the frequency and intensity of coastal flood events, posing risks to coastal communities and infrastructure. While regional climate adaptation investments can provide substantive flood protection, existing plans often neglect uncertainty in future climate conditions and adaptation performance, consequently neglecting the option value of flexibly implementing proposed projects. Addressing this gap, we develop and employ a generalizable real options analysis (ROA) valuation framework that considers how uncertainty in adaptation project costs, SLR, flood severity, and flood losses inform the full range of adaptation performance outcomes. We further propose and apply a novel, computationally efficient flood loss sampling algorithm to estimate the consequences of randomly arriving coastal flood events. We apply this ROA framework to assess the option value of flexibly timing adaptation investments over time, investigating an adaptation pathway proposed by the City of Boston from the perspective of the regional transit system manager. Our results suggest that flexible implementation can provide significant option value in the near- to mid-term (>30 years), with the highest option values under low-probability, high-consequence scenarios. Our results also suggest adaptation pathway performance in the latter half of the 21st century is most sensitive to uncertainty in SLR, flood loss estimates, and flood frequency, underscoring the importance of uncertainty quantification in the long-term valuation of adaptation investments.