Prospective Life Cycle Assessment (LCA) is a relevant approach to assess the environmental performance of future energy pathways. Amongst different types of prospective scenarios, cornerstone scenarios meant for complex systems and long-term approaches, are of interest to assess such performance. They rely on different types of long-term projections, such as projections of technological evolutions and of energy resources. In most studies, scenarios are defined with single values for each parameter, and environmental impacts are assessed in a deterministic way. Inherent uncertainties related to these prospective assumptions are not considered and prospective LCA uncertainties are thus not addressed. In this paper we describe a methodology to account for these uncertainties and to identify the parameters inducing most of the uncertainties in the prospective LCA results. We apply this approach to prospective LCAs of photovoltaic-based electricity generation systems.