This research evaluates the life cycle cost (LCC) of different Modern Methods of Construction (MMC) for affordable housing. Specifically, it investigates the impact of commonly used 2D primary structural systems on the life cycle of a standard affordable housing design in the UK, comparing the results to conventional brick houses. Data from BIM and EDGE software were utilised to estimate the construction, operational, and maintenance costs of the various construction methods and the overall LCC of the houses. The study conducted a comprehensive life cycle cost analysis of the four systems, comparing the results to identify cost differentials. The findings indicate that while the construction (10–16%) and maintenance (13–38%) costs of MMCs are slightly higher compared to conventional houses, the operational costs (55–67%) of MMCs are significantly lower. This cost reduction is attributed to the improved airtightness and insulated thermal performance of MMCs, resulting in substantial energy cost savings over the lifespan of the housing. Moreover, the research demonstrates that the overall life cycle costs of MMC-based housing are 30–42% lower than those of similar conventional brick houses. These results emphasise that appropriate implementation of modern construction methods enhances affordability and improves the sustainability of both houses and households. This study provides valuable insights into the cost dynamics of different construction methods for affordable housing. Stakeholders can make informed decisions to promote cost-effective, sustainable, and affordable housing solutions by considering the life cycle cost and energy efficiency aspects.