This article evaluates the implications of uncertainty in the life cycle (LC) energy efficiency and greenhouse gas (GHG) emissions of rapeseed oil (RO) as an energy carrier displacing fossil diesel (FD). Uncertainties addressed include parameter uncertainty as well as scenario uncertainty concerning how RO coproduct credits are accounted for (uncertainty due to modeling choices). We have carried out an extensive data collection to build an LC inventory accounting for parameter uncertainty. Different approaches for carbon stock changes associated with converting set-aside land to rapeseed cultivation have been considered, which result in different values: from −0.25 t C/ha.yr (carbon uptake by the soil in tonnes per hectare year) to 0.60 t C/ha.yr (carbon emission). Energy renewability efficiency and GHG emissions of RO are presented, which show the influence of parameter versus scenario uncertainty. Primary energy savings and avoided GHG emissions when RO displaces FD have also been calculated: Avoided GHG emissions show considerably higher uncertainty than energy savings, mainly due to land use (nitrous oxide emissions from soil) and land use conversion (carbon stock changes). Results demonstrate the relevance of applying uncertainty approaches; emphasize the need to reduce uncertainty in the environmental life cycle modeling, particularly GHG emissions calculation; and show the importance of integrating uncertainty into the interpretation of results.