The neuropathic pain is the key feature of Fabry disease and has a severe impact on the quality of life. However, as to ineffective or renal involvement, only anticonvulsants can be used, even it also shows big side effect. Calcium ions play a fundamental role in several biological processes. As the marker of Fabry disease, globotriaosylsphingoshine enhances calcium currents in dorsal root ganglia neurons. Moreover, evidences have accumulated for the efficacy of sirolimus in blocking calcium influx. Here we investigate the efficacy of sirolimus on neuropathic pain in Fabry disease. First, plantar test was investigated. Sirolimus recovered the Fabry mice thermal sensitivity to normal. However, it shows opposite function against wild type mice. 1% voltaren only works on wild type but not the Fabry mice. Second, to clarify the calcium ions currents in vivo, manganese-enhanced MRI (MEMRI) was performed. With heat stimulation, there are much more accumulated manganese ions in Fabry mice brain. 0.2% sirolimus reduced the manganese ions’ concentration in Fabry but increased it in wild type mice. Third, α-gal A CRISPR/Cas9 KO plasmid and HDR plasmid were co-transfected into SK-N-MC, U-87 MG, F11 and normal human dermal fibroblasts (NHDF). Then calcium influx was determined by Fura-2. Only knockout neurons, SK-M-MC and F11 but not U-87 MG and NHDF increased calcium influx in response to glutamate or capsaicin. Sirolimus totally inhibited the calcium flux into SK-N-MC but F11, U-87 MG and NHDF. At last, the western blot and quantity real-time PCR were performed. Sirolimus fulfilled the similar efficacy to voltaren on nerve growth factor (NGF). However, it revealed different function against brain-derived neurotrophic factor (BDNF). It increased the activity of cAMP response element binding protein (CREB) to enhance BDNF transcription and blocked CaMKIIα to release the BDNF to the serum. Combining all results, sirolimus might be a useful alternative for clinical neuropathic pain management in Fabry disease.