The maritime transportation sector (MTS) is undertaking a major global effort to reduce emissions of greenhouse gases (GHG), e.g., sulfur oxides, nitrogen oxides, and the concentration of particulates in suspension. Substantial investment is necessary to develop alternative sustainable fuels, engines, and fuel modifications. The alternative fuels considered in this study include liquified natural gas, nuclear energy, hydrogen, electricity, and biofuels. This paper focuses on biofuels, in particular fast pyrolysis bio-oil (FPBO), a serious partial alternative in MTS. There are some drawbacks, e.g., biofuels usually require land necessary to produce the feedstock and the chemical compatibility of the resulting biofuel with current engines in MTS. The demand for sustainable feedstock production for MTS can be overcome by using cellulose-based and agroforestry residues, which do not compete with food production and can be obtained in large quantities and at a reasonably low cost. The compatibility of biofuels with either bunker fuel or diesel cycle engines can also be solved by upgrading biofuels, adjusting the refining process, or modifying the engine itself. The paper examines the possibilities presented by biofuels, focusing on FPBO in Brazil, for MTS. The key issues investigated include FPBO, production, and end use of feedstocks and the most promising alternatives; thermal conversion technologies; potential applications of FPBO in Brazil; sustainability; biofuels properties; fuels under consideration in MTS, challenges, and opportunities in a rapidly changing maritime fuel sector. Although the focus is on Brazil, the findings of this paper can be replicated in many other parts of the world.