Transportation networks with intrinsic flow dynamics governed by the Kirchhoff's current law are ubiquitous in natural and engineering systems. There has been recent work on designing optimal transportation networks based on biological principles with the goal to minimize the total dissipation associated with the flow. Despite being biologically inspired, e.g., adaptive network design based on slime mold Physarum polycephalum, such methods generally lead to suboptimal networks due to the difficulty in finding a global or nearly global optimum of the nonconvex optimization function. Here we articulate a design paradigm that combines engineering control and biological principles to realize optimal transportation networks. In particular, we show how small control signals applied only to a fraction of edges in an adaptive network can lead to solutions that are far more optimal than those based solely on biological principles. We also demonstrate that control signals, if not properly designed, can lead to networks that are less optimal. Incorporating control principle into biology-based optimal network design has broad applications not only in biomedical science and engineering but also in other disciplines such as civil engineering for designing resilient infrastructure systems.