As part of the global efforts to make aviation activities more environmentally friendly, the worldwide goal is to achieve a 50% reduction in the 2005 emissions by 2050. In this context, aviation emissions represent a critical challenge to aviation activities, especially with the increasing travel demand up to the beginning of the COVID-19 crisis, starting in 2020. One of the potential drivers that would help the aviation industry reduce its emissions is the use of sustainable aviation fuel (SAF). In this study, we analyzed the impact of SAF from an air traffic flow management (ATFM) perspective, considering delay and re-routing costs. We developed an optimization model that considers, in addition to the traditional ATFM costs, fuel costs and carbon dioxide emissions. We investigated the impact of accounting for these two new aspects, that is, fuel costs and emissions, on ATFM performance, and we compared SAF with conventional fuel. The analysis of a real case study revealed that, in addition to delay and re-routing costs, fuel cost should be included in the ATFM model so that the resulting solution becomes economically and environmentally realistic for airlines. The increase in the fuel cost and network delays when using SAF requires setting an appropriate carbon price under an emission policy, such as the carbon offsetting and reduction scheme for international flights policy, to make SAF more attractive. Furthermore, flexible re-routing programs for flights operated using SAF make it advantageous from an ATFM perspective.