The study aims to test the effect of transdermal application of azithromycin in the prevention of skin flap infection in experimental rats. The accumulative penetration quantities of azithromycin through excised rat skin and the azithromycin quantities in flap tissues from rats given 1%, 2%, and 3% azithromycin gels were assayed by UV spectrophotometer. Staphylococcus aureus and pathogenic Escherichia coli were inoculated to the underneath of the random ischemic rat flaps to induce bacterial infection. The azithromycin gels were applied on the flaps daily for 7 days. The survival areas of flaps were measured by planimetry. The accumulative penetration quantities of azithromycin and the azithromycin quantities in flap tissues increased in a time-dependent manner (P < 0.05). Azithromycin gels decreased the inflammatory reaction and enhanced the survival area of flaps (P < 0.05). We concluded that 1% azithromycin gel could penetrate into the flap tissues and significantly increase survival area of infected flaps.