Despite significant advances in the design optimization of bone scaffolds for enhancing their biomechanical properties, the functionality of these synthetic constructs remains suboptimal. One of the main challenges in the structural optimization of bone scaffolds is associated with the large uncertainties caused by the manufacturing process, such as variations in scaffolds’ geometric features and constitutive material properties after fabrication. Unfortunately, such non-deterministic issues have not been considered in the existing optimization frameworks, thereby limiting their reliability. To address this challenge, a novel multiobjective robust optimization approach is proposed here such that the effects of uncertainties on the optimized design can be minimized. This study first conducted computational analyses of a parameterized ceramic scaffold model to determine its effective modulus, structural strength, and permeability. Then, surrogate models were constructed to formulate explicit mathematical relationships between the geometrical parameters (design variables) and mechanical and fluidic properties. The Non-Dominated Sorting Genetic Algorithm II (NSGA-II) was adopted to generate the robust Pareto solutions for an optimal set of trade-offs between the competing objective functions while ensuring the effects of the noise parameters to be minimal. Note that the nondeterministic optimization of tissue scaffold presented here is the first of its kind in open literature, which is expected to shed some light on this significant topic of scaffold design and additive manufacturing in a more realistic way.