Previous reports indicate that the immunosuppressant FK506 protects the nervous system upon several kinds of injuries both in vivo and in vitro. However, the mechanisms involved in said neuroprotective effect remain to be determined. We investigated the effects of FK506 on the axonal degeneration induced by axotomy of the Drosophila wing and its potential mechanisms. After a complete transection of the adult wing, we examined structural changes in glutamatergic neurons expressing GFP at the L1 nerve. Four days post axotomy, the L1 nerve width was significantly reduced (42% respect to uninjured wing). Immediately after the axotomy flies received vehicle or different concentrations of FK506 for 4 days. Toxicity studies showed that 0.01 to 1 µM FK506 treatments did not alter the adult fly survival. After 4 days, treatment with 0.1 or 1 µM FK506 reduced the nerve damage in 39 and 21%, respectively. In contrast, the lower concentration of FK506 (0.01 µM) did no effect on nerve damage, although it did increase the number of neuronal somas in the L1 nerve of injured wings when compared to uninjured ones. The overexpression of a wild-type allele of dfkbp59, enhanced the neuroprotective effect of 0.1 µM FK506, without altering the number of neuronal somas. In conclusion, dFKBP59 might be contributing to the in vivo neuroprotective effect of FK506 in this model of axotomy-induced neurodegeneration. The wing axotomy paradigm appears to be suitable to elucidate the underlying in vivo neuroprotective mechanisms of FK506.