Civil marine reactors face a unique set of design challenges. These include requirements for a small core size and long core lifetime, a 20% cap on fissile loading, and limitations on using soluble neutron absorbers. In this reactor physics study, we seek to design a core that meets these requirements over a 15 effective full-power-years (EFPY) life at 333 MWth using homogeneously mixed all-UO2 and micro-heterogeneous ThO2-UO2 duplex fuels. In a companion (Part I) paper, we found assembly designs using 15% and 18% 235U for UO2 and duplex fuels, respectively, loaded into 13 × 13 pin arrays. High thickness (150 μm) ZrB2 integral fuel burnable absorber (IFBA) pins and boron carbide (B4C) control rods are used for reactivity control. Taking advantage of self-shielding effects, these designs maintain low and stable assembly reactivity with little burnup penalty.In this paper (Part II), whole-core design analyses are performed for small modular reactor (SMR) to determine whether the core remains critical for at least 15 EFPY with a reactivity swing of less than 4000 pcm, subject to appropriate constraints. The main challenge is to keep the radial form factor below its limit (1.50). Burnable poison radial-zoning is examined in the quest for a suitable arrangement to control power peaking. Optimized assemblies are loaded into a 3D reactor model in PANTHER. The PANTHER results confirm that the fissile loadings of both fuels are well-designed for the target lifetime: at the end of the ∼15-year cycle, the cores are on the border of criticality. The duplex fuel core can achieve ∼4% longer core life, has a ∼3% lower initial reactivity and ∼30% lower reactivity swing over life than the final UO2 core design. The duplex core is therefore the more successful design, giving a core life of ∼16 years and a reactivity swing of less than 2500 pcm, while satisfying all the neutronic safety parameters. In particular, one of the major objectives of this study is to offer/explore a thorium-based candidate alternative fuel platform for the proposed marine core. It is proven by literature reviews that the ability of the duplex fuel was never explored in the context of a single-batch, LEU, SBF, long-life SMR core. In this regard, the motivation of this paper is to understand the underlying physics of the duplex fuel and ‘open the option’ of designing the functional cores with both the duplex and UO2 fuel cores.