Greenhouse gas (GHG) emissions from the combustion of fossil energy need to be reduced to combat global climate change. For zero energy and Zero Emission Buildings (ZEB), photovoltaic solar energy systems are often installed. When the goal is to build a life cycle Zero Emission Building, all emissions come under scrutiny. Emissions from photovoltaic (PV) energy systems in Zero Emission Buildings have been shown to have a relative large share of material emissions. In this paper, we compare GHG emissions per kW h of electricity and greenhouse gas emission payback times (GPBT) for three residential PV systems in Zero Emission Pilot Buildings in Norway. All the buildings have roof mounted PV systems with different design solutions. The objective is to analyse the emission loads and GPBT of these three systems to facilitate for more informed choices of energy systems for Zero Emission Buildings. The results show that the total embodied emissions allocated per square meter of module area are around 150–350 kg CO2 eq/m2 for the three different systems. Emissions from the mounting systems vary from 10 to 25 kg CO2 eq/m2 depending on the material types and quantities used. When modules replace other roofing materials, such as roof tiles, mounting emissions were reduced by approximately 60%. GHG emissions per kW h electricity produced were in the range of 30–120 g CO2 eq/kW h for the different systems. The system with the lowest emissions was the largest system, which had a simple mounting structure and modules with reused cells. It was found that the GPBT was strongly dependent on the scenario used for electricity grid emissions. By applying a dynamic emission payback scenario with an optimistic reduction of emissions from the European electricity grid, the GPBT was 3–8 years for the different systems. When comparing the emissions with current Norwegian hydropower emissions, of around 20 g CO2 eq/kW h, it was found that all of the PV system’s emissions were higher. When compared to a mainly fossil fuel based grid, all the PV system’s emissions are low. This study highlights the importance of reliable emission documentation for PV modules and their mounting structures on the market.