Construction schedule optimisation problems have been explored extensively, including activity sequencing rules and work packaging. Yet knowledge is still lacking in the sequencing of mechanical, electrical and plumbing (MEP) components with geometric complexity, and how to handle conflicting precedence between MEP work packages arising from the geometric complexity. Another concept of interest is working zones, which are spaces a building may be divided into to enable parallel working: they have the potential to reduce idle working space and project duration, but its integration with the scheduling of MEP systems and effect on schedule optimisation are under-investigated. This work studies the optimisation of construction schedules for building structural and MEP systems considering working zones. First, a conceptual framework is developed, on: (1) activity sequencing rules, featuring preferences on spatial proximity and component size for MEP components; (2) clustering and cluster-splitting method, to resolve the conflicts among MEP packages; and (3) mathematical formulation of schedule optimisation problems as mixed-integer linear programming (MILP) problems. Next, a software tool consisting of an Excel add-in, a MATLAB executable programme and an Excel macro is developed to implement the framework. Two case studies are carried out. The results of case studies and further analysis demonstrate the large potential of zones in reducing project duration, the effect of the amount of resource available, and strategies for future scheduling practices. Applicability to general construction projects, limitations and future directions are also discussed.