Fibroblast growth factor 21 (FGF21) is a crucial regulator of glucose and lipid metabolism, showing significant therapeutic promise for metabolic disorders. However, its clinical application is limited by poor pharmacokinetics. One potential strategy to improve its half-life is to facilitate albumin binding through fatty acid derivation. Despite this promise, achieving site-specific modifications of FGF21 while preserving its biological activity has been challenging. In this study, we applied a rational design approach to create site-specific fatty acid derivatives of FGF21, guided by the structure of the FGF21-receptor complex. This strategy successfully enhances albumin binding without interfering with receptor interactions. The modified FGF21 derivatives exhibited dramatically extended half-lives in mice, increasing from 0.73 h to 11.36 and 13.36 h, respectively. Furthermore, these analogues showed superior biological activity in the presence of albumin, outperforming the C-terminal-derived variant zalfermin. This rational design approach not only improves the pharmacokinetic profile of FGF21 but also provides a framework for enhancing the therapeutic potential of other small proteins.