Enhancing the sustainability of activities is an undebatable need for decision makers regarding the economy as well as society. Fuel cells and their application in different areas, such as energy supply or mobility, are viewed as a promising means towards more sustainability. However, fuel cells as well as fuel-cell-based application systems cause a couple of possibly conflictive impacts in terms of ecological, economic, and social targets—their positive contribution to sustainability is not confident. Consequently, a significant assessment of sustainability is needed to enable a targeted development of fuel cells and their application systems, including the selection of alternative design variants. Furthermore, such assessment is necessary to provide evidence for the intended improvements and thereby contribute to market success and implementation of the systems. However, an overview of the existing methods for sustainability-related assessment of fuel cells and fuel-cell-based systems as well as the outcomes of the assessments does not exist. Therefore, a systematic literature review is conducted without restriction of fuel cell types and evaluation methods. Such a comprehensive overview does not yet exist to the best of the authors’ knowledge. With regard to the suggested or applied methods, the results show, amongst others, that the economic assessment does not refer to the methodical state-of-art, the social dimension is neglected, and an overall assessment of sustainability, aggregating all three dimensions, is not conducted. Due to the variety of analyzed objects as well as applied methods, the outcomes of the studies provide not more than scattered knowledge about the relevance of components and the advantageousness of fuel cells, their variants, and their application systems regarding sustainability. To contribute to avoiding methodological deficiencies, a procedure model for an integrated assessment is presented.