Our previous study demonstrated that sepsis may decrease the activity of acetylcholinesterase (AChE) at the neuromuscular junction (NMJ) of the diaphragm at 24 h, and thus improve the antagonistic action of neostigmine on rocuronium. The present study aimed to determine the effects of sepsis on AChE activity over 2 weeks, which is a more clinically relevant time period. Furthermore, the present study aimed to elucidate the association between AChE activity and its expression at the NMJ during sepsis. Male adult Sprague‑Dawley rats were randomly divided into the sham or sepsis groups. Sepsis was induced by cecal ligation and puncture. On days 1, 3, 7 and 14 after surgery, AChE activity at the NMJ of the diaphragm was detected using a modified Karnovsky and Roots method. Furthermore, AChE expression levels at the NMJ, and in the whole muscle fibers of the diaphragm, were detected by immunohistofluorescence staining and western blot analysis, respectively. AChE activity was significantly decreased in the sepsis group, with its lowest level detected on day 7; however, its activity had partially recovered on day 14 (P<0.01). AChE activity was positively correlated (r=0.975, P=0.025) with its expression at the NMJ, which showed a similar trend over 2 weeks of sepsis. The protein expression levels of AChE in the whole muscle fibers of the diaphragm were significantly decreased on days 1, 3 and 7 in the sepsis group (P<0.01), with the lowest level observed on day 3. In conclusion, sepsis decreased AChE activity by reducing its expression at the NMJ over 14 days; the reduced expression of AChE at the NMJ might be as a result of its reduced muscular production.