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AbstractThe methodology described in this article enables a type of holistic fleet optimization that simultaneously considers the composition and activity of a fleet through time as well as the design of individual systems within the fleet. Often, real‐world system design optimization and fleet‐level acquisition optimization are treated separately due to the prohibitive scale and complexity of each problem. This means that fleet‐level schedules are typically limited to the inclusion of predefined system configurations and are blind to a rich spectrum of system design alternatives. Similarly, system design optimization often considers a system in isolation from the fleet and is blind to numerous, complex portfolio‐level considerations. In reality, these two problems are highly interconnected. To properly address this system‐fleet design interdependence, we present a general method for efficiently incorporating multi‐objective system design trade‐off information into a mixed‐integer linear programming (MILP) fleet‐level optimization. This work is motivated by the authors' experience with large‐scale DOD acquisition portfolios. However, the methodology is general to any application where the fleet‐level problem is a MILP and there exists at least one system having a design trade space in which two or more design objectives are parameters in the fleet‐level MILP.