We investigated the range and frequency of significant adverse events (AEs) in use of pharmacopuncture and acupuncture using large-scale, single-center safety data as evidence supporting safety of acupuncture with pharmacopuncture, used extensively in Asia, is scarce. Status reports (nurse records in ambulatory and inpatient care units, and administrative event records) as a part of an internal audit at a Korean Medicine hospital specializing in the treatment of musculoskeletal disorders, patient complaints filed through the hospital website, and medical records of patients visiting from December, 2010 (inception of internal audit) to October, 2014 were retrospectively reviewed. A total 80,523 patients (5966 inpatients and 74,557 outpatients) visited during this period. Inpatients received an average 31.9 ± 20.7 acupuncture, 23.0 ± 15.6 pharmacopuncture, and 15.4 ± 11.3 bee venom pharmacopuncture sessions, and outpatients were administered 8.2 ± 12.2 acupuncture, 7.8 ± 11.5 pharmacopuncture, and 10.0 ± 12.3 bee venom sessions, respectively. AEs associated with acupuncture/pharmacopuncture were forgotten needle (n = 47), hypersensitivity to bee venom (n = 37), presyncopic episode (n = 4), pneumothorax (n = 4), and infection (n = 2). Most cases were mild requiring little or no additional intervention and leaving no sequelae. Although serious AEs including infection (n = 2) and anaphylaxis associated with bee venom treatment (n = 3) were also reported, incidence was rare at 0.002% in infection and 0.019% in anaphylaxis. Incidence of AEs associated with acupuncture/pharmacopuncture treatment was low, and most cases were not serious. Still, however rare, avoidable AEs can and should be prevented through education and corrective action. Further prospective studies on the effect of error reduction strategies on incidence of adverse effects are warranted.