Chronic cerebral hypoperfusion (CCH) is damaging to white matter in the brain. So far few studies have investigated long-term axonal damage following CCH. The aim of this study was to investigate the involvement of neurofilament 200 (NF200) and amyloid-β (1-40) [Aβ (1-40)] in the pathological mechanism for neuronal damage, and to quantify changes in their expression over time in a rat model of CCH. A rat model of CCH was established using partial bilateral ligation of the common carotid arteries. The extent of stenosis was verified by measuring the changes in cerebral blood flow after surgery. Histology was used to assess hippocampal neuronal pathology, and immunohistochemistry was used to quantify the expression of NF200 and Aβ (1-40) at 2, 4, and 12 weeks after surgery. The cerebral blood flow reduced to 33.89 ± 5.48 % at 2 weeks, 36.83 ± 4.63 % at 4 weeks and 51.44 ± 4.90 % at 12 weeks. Immunofluorescence staining of neuronal perikarya sections revealed a marked decrease in the population of surviving pyramidal cells in the hippocampal CA1 region, a significant up-regulation in the expression of Aβ (1-40), and a significant reduction in the expression of NF200 following CCH surgery. Moreover, this trend was increasingly obvious over time. Our data demonstrate that CCH leads to axonal damage over time. We also confirmed that the expression of Aβ (1-40) and NF200 may be useful biomarkers of axonal damage following CCH.