Molecular modification with polyethylene glycol (PEGylation) is an effective approach to improve protein biostability and decrease protein immunogenic activity. To create a PEGylated recombinant human acid fibroblast growth factor (rhaFGF) and improve its bio-stability, we have produced a rhaFGF mutant (rhaFGF(ser98,132)) by replacing the 98th and the 132nd cysteine residues with serine residues. The rhaFGF(ser98,132) that retains the bioactivity of rhaFGF was then site-specifically conjugated with PEG-maleimide at the 31st cysteine residue. PEGylated rhaFGF(ser98,132) has less effect than the native rhaFGF(ser98,132) on stimulating 3T3 cell proliferation in vitro; however, its biostability at a prolonged incubation under various temperatures and resistance to trypsinization were significantly enhanced, and half-life time in vivo was elongated while its immunogenicity was significantly decreased. The physiological function of PEGylated rhaFGF(ser98,132) was evaluated in a rat model of retinal ischemia/reperfusion injury, showing that in vivo supplementation of PEGylated rhaFGF(ser98,132) provided a significantly better protection than the native rhaFGF(ser98,132) against ischemia/reperfusion-induced retinal morphological changes and lipid peroxidation. The protection is probably mediated by antioxidant protective mechanisms.