Essential enzymes in redox reactions, flavin reductases take part in a variety of cellular functions such as electron transport, biosynthesis, and detoxification. In this work, we conducted a comprehensive in silico characterization of a novel flavin reductase-like protein, REF, to examine its ligand-binding characteristics, structural organization, and evolutionary conservation. According to sequence-based domain analysis, REF is part of the flavin reductase-like domain and the FMN-binding split-barrel superfamily, indicating catalytic activity that is dependent on FMN. With conserved secondary structural elements and an RMSD in line with functional conservation, tertiary structure prediction showed that REF and a reference flavin reductase shared a high degree of structural similarity. Comparable molecular weights, isoelectric points, and hydropathicity were found by physiochemical analysis; however, REF showed a lower instability index, indicating greater structural stability. Strong binding affinity for both proteins was found by molecular docking of flavin mononucleotide (FMN), with REF showing a marginally higher predicted affinity (-9.1 kcal/mol) than flavin reductase (-8.8 kcal/mol). According to these results, REF shows modifications that could improve FMN binding while maintaining the structural integrity of flavin reductases. This study lays the groundwork for further experimental validation while highlighting the evolutionary and functional implications of such adaptations.