Conventional therapies for diseases that are associated with protein aggregation typically prevent rather than clear protein aggregates. We have proposed neutron dynamic therapy (NDT) as a physical clearance therapy for protein aggregates. Advanced glycation end-products (AGEs), which are aggregated proteins, have been implicated in diabetes, Alzheimer's, and heart disease. Herein, we report the use of the boron tracedrug UTX-51, under thermal neutron irradiation, as an NDT for the targeted clearance of glycated bovine serum albumin (Gly-BSA), a model of AGEs. Sodium dodecyl sulfate-polyacrylamide gel electrophoresis was performed to detect Gly-BSA decomposition by thermal neutron irradiation treated with UTX-51. The combination of UTX-51 with neutron irradiation showed a decrease in band intensity of Gly-BSA. We present our NDT strategy, which has been used for the targeted clearance of Gly-BSA, suggesting that NDT with boron tracedrugs can be used for the treatment of AGEs-related disease.