Purpose The purpose of this study was to investigate sub-chronic toxicity of scolopendrid pharmacopuncture in mouse and method of increasing output of scolopendrid pharmacopuncture. Methods In order to prove the clinical safety of scolopendrid pharmacopuncture during 90 days, We have observed the physical reaction(side effect) and clinical pathology test after scolopendrid pharmacopuncture treatment and investigated method of increasing Output of scolopendrid pharmacopuncture for 90%, 80%, 70% ethanol. Results In subchronic toxicity test, there was no significant sign in clinical sign, opthalmological values, body weights, hematological values and urinalysis values. And we could see that food consumptions and water consumptions increased significantly, albumin, triglycerides, GPT in blood chemical values and Liver, Testis(right) in organ weights changed significantly in some groups, compared with those in the S1 group. But these changes were observed within the scope of physiology. So there was no sign of toxication in subchronic toxicity test, and we can tell that NOAEL(No Observed Adverse Effect Level) is above 0.286mg/kg/day. And 70% ethanol solution of scolopendrid was yielded the most amount of substance. Conclusions This study demonstrates that scolopendrid pharmacopuncture is to treatment of safety for a long time and we can obtain much amount from 70% ethanol solution of scolopendrid.