Strategies, models, and algorithms facilitating such models are explored to provide transportation network managers and planners with more flexibility under uncertainty. Network design problems with non-stationary stochastic OD demand are formulated as real option investment problems and dynamic programming solution methodologies are used to obtain the value of flexibility to defer and re-design a network. The design premium is shown to reflect the opportunity cost of committing to a “preferred alternative” in transportation planning. Both network option and link option design problems are proposed with solution algorithms and tested on the classical Sioux Falls, SD network. Results indicate that allowing individual links to be deferred can have significant option value. A resource relocation model using non-stationary stochastic variables as chance constraints is proposed. The model is applied to air tanker relocation for initial attack of wildfires in California, and results show that the flexibility to switch locations with non-stationary stochastic variables providing 3-day or 7-day forecasts is more cost-effective than relocations without forecasting. Due to the computational costs of these more complex network models, a faster converging heuristic based on radial basis functions is evaluated for continuous network design problems for the Anaheim, CA network with a 31-dimensional decision variable. The algorithm is further modified and then proven to converge for multi-objective problems. Compared to other popular multi-objective solution algorithms in the literature such as the genetic algorithm, the proposed multi-objective radial basis function algorithm is shown to be most effective. The algorithm is applied to a flexible robust toll pricing problem, where toll pricing is proposed as a strategy to manage network robustness over multiple regimes of link capacity uncertainty. A link degradation simulation model is proposed that uses multivariate Bernoulli random variables to simulate correlated link failures. The solution to a multi-objective mean-variance toll pricing problem is obtained for the Sioux Falls network under low and high probability seasons, showing that the flexibility to adapt the Pareto set of toll solutions to changes in regime-e.g. hurricane seasons, security threat levels, etc.-can increase value in terms of an epsilon indicator.