Rationale:Congenital butyrylcholinesterase deficiency (BCHED) is a rare autosomal recessive genetic disorder caused by a pathogenic mutation in the BCHE gene. Patients with BCHED may experience prolonged apnea or even death after the application of drugs such as succinylcholine. We aimed to identify the genetic basis of disease in a patient presenting with butyrylcholinesterase deficiency in order to confirm the diagnosis, expand BCHE gene mutation spectrum, and elucidate potential genotype-phenotype associations to inform management.Patient concerns:A 51-year-old woman presented with “vague pain in the upper and middle abdomen.” Her serum cholinesterase level was 211 U/L (reference value 4000–13,000 U/L). Other laboratory findings were normal. Genetic analysis revealed compound heterozygous mutations in BCHE gene, which was considered pathogenic in this case.Diagnoses:The patient presented with low serum cholinesterase levels, which excluded common causes such as liver disease, drug toxicity, and chronic illness. Whole exon examination revealed compound heterozygous mutations in the BCHE gene; thus, the patient was diagnosed with congenital BCHED.Interventions:Gastroscopy without succinylcholine or mivacurium chloride was recommended. The gastroscopy results were “gastric polyps,” and gastroscopic “polypectomy” was performed. The patient was advised to avoid succinylcholine use.Outcomes:The patient’s serum cholinesterase level was reviewed 3 months later, and the result was 215 U/L. Double heterozygous mutations are the cause of BChE deficiency of this woman in this study, including a novel mutation NM_000055.4: c.666_669del (p.Phe223Glufs*38). A review of the literature reveals considerable variation in the hotspot variants of the BCHE gene across different populations. The Chinese population displays a higher prevalence of the silent type, which is more sensitive to anesthetics such as succinylcholine.Lessons:Clinical manifestations of congenital BCHED were not significant. This study avoided a potential anesthetic accident, and the novel variant enriched the BCHE gene mutation spectrum.