This paper presents an analysis of how the design of a photovoltaic (PV) system influences the greenhouse gas emission balance in a net zero emission building (nZEB). In a zero emission building, the emissions associated both with the energy required in the operation of the building (operational emissions) and the energy used to produce the building materials (embodied emissions) are offset by renewable energy generated on-site (avoided emissions). The analysis is applied to a nZEB concept for a single-family building, developed by the Norwegian Research Centre on Zero Emission Buildings. Previous analyses have shown that the installation of a PV system accounts for a significant share of the embodied emissions of a nZEB. The objective of this paper is to assess how the PV system design choices influence the embodied and avoided emissions, in order to determine how the environmental impact can be minimised. Four different PV technologies (Si-mono, poly-Si and CIS, and high-efficiency Si-mono) in four different system designs for flat roofs are evaluated using two different grid emission factors. The installations are compared by means of net avoided emissions, greenhouse gas payback time (GPBT), greenhouse gas return on investment (GROI), and finally the net emission balance of the building. The results show that the system with the largest area of high-efficiency Si-mono modules achieves the best lifetime emission balance, but that the greenhouse gas return on investment is highest for the optimally oriented CIS modules.