The increasing complexity of modern naval vessels due to technological advancements poses challenges for early-stage ship design (ESSD). Developing well-defined system architectures and adopting systems engineering approaches are essential to address these challenges. Model-based systems engineering (MBSE) has emerged as a solution to the issues inherent in traditional document-centric methods and is considered the future of systems engineering. This paper aims to address the barriers to MBSE adoption by exploring its value in the early design stage of naval vessels. The paper focuses on system architecture development, covering operational, functional, logical, and physical perspectives, and evaluates two MBSE tools: Capella and CDP4-COMET. The analysis demonstrates that both tools effectively validate anticipated benefits, concluding that MBSE can enhance and accelerate ESSD, with Capella performing better in the early design stages and CDP4–COMET excelling in the later stages. This paper, thus, differentiates itself from traditional performance and detailed design modeling, such as those addressing motion, control, or thermal dynamics.