The immunosuppressant FK506 protects the nervous system upon several kinds of injuries both in vivo and in vitro. However, the properties and mechanisms involved in its neuroprotective effect remain obscure. Here we aimed to investigate the effects of FK506 in the neurodegeneration induced by an in vivo axotomy on the L1 nerve of Drosophila adult wing. After a complete transection of the L1 nerve on the right wing, we examined the structural changes in glutamatergic neurons expressing GFP. The left wing was left intact and used as an internal control. To evaluate the injury, we developed a quantification system based on objective continuous variables to replace the discrete categorization commonly used. Four days post-axotomy, injured L1 nerves displayed a 39% width reduction and increased number of small highly-circular particles when compared to intact wings. Immediately after the axotomy, adult flies received either vehicle or FK506 for 4 days. Toxicity studies showed that 0.01 to 1 µM FK506 treatments did not alter the adult fly survival. Neither 0.01 µM nor 0.1 µM FK506 treatments affected the nerve width loss. However, 0.01 µM FK506 reduced the axonal fragmentation and the probability of small highly-circular particles. In conclusion, the quantitative analysis in the wing axotomy paradigm revealed specific properties in the neuroprotective effect of FK506 in vivo. Future studies will examine specific mechanisms involved in such effects of FK506 on axonal fragmentation.