Acupuncture has been used in clinical trials for the treatment of abdominal pain in patients with irritable bowel syndrome (IBS). However, scientific evidence is still lacking and the underlying mechanism remains largely unexplored. The aim of this study was to examine the effects of repeated administration of electro-acupuncture (EA) on chronic visceral hypersensitivity and on the phosphorylation of spinal cord N-methyl-D-aspartic acid (NMDA) receptors in a rat model of IBS. The results showed that repeated administration of EA at bilateral points of Zu-san-li (ST-36) and Shang-ju-xu (ST-37) significantly attenuated chronic visceral hypersensitivity induced in young adult rats by neonatal colon irritation. Such an effect was not seen in either of the two controls: sham-EA at ST-36 and ST-37 without electrical stimulation and EA at control points (BL-62 and tail). Furthermore, rats with chronic visceral hypersensitivity exhibited high-level expression of phosphorylated NMDA receptor subunit 1 (pNR1) in the spinal cord (L4-L5 segments), which was markedly attenuated by EA treatment. In addition, EA at ST-36 and ST-37 neither altered the pain threshold of normal rats nor affected the expression of pNR1 in the lumbosacral spinal cord. Altogether, these data indicate that the EA-mediated attenuation of chronic visceral hypersensitivity is correlated with the down-regulation of NMDA receptors phosphorylation at the spinal level.