In this study, chemical modification of recombinant hirudin variant-2 (HV2) with palmitic acid (PAL) was proposed as an alternative approach to circumvent the limitations of PEGylation. To facilitate a sufficient contact of the hydrophilic HV2 to the hydrophobic PAL, thereby improving the reaction specificity to achieve the desired mono-PAL-HV2 with high retained bioactivity, the reaction was developed in mixed aqueous-organic solutions. Compared with HV2 conjugation with PAL-benzotriazole (PAL-BTA) in mixed aqueous-NMP solution, the conjugation of HV2 with PAL-N-hydroxysuccinimide (PAL-NHS) in mixed aqueous-DMSO solution could improve the site-specific conjugation of one PAL molecule to a particular lysine residue. Furthermore, the reaction mixture of the latter was further purified by preparative liquid chromatography. Three mono-PAL-HV2 isomers were obtained and retained 36%, 4% and 89% of the in vitro anticoagulant activity of unmodified HV2, respectively. One of the mono-PAL-HV2 isomers, namely, mono-PAL-HV2-3, was isolated with the highest selectivity and exhibited the highest in vitro anticoagulant bioactivity. Modification site analysis of mono-PAL-HV2-3 revealed that a single PAL molecule was conjugated at Lys27 of HV2. This study presented a successful PAL modification in which site-specific reaction was improved to achieve the desired mono-PAL-HV2 with highly retained bioactivity in mixed aqueous-organic solutions.