Rationale: Lipid storage myopathies (LSMs) are a series of genetic disorders of lipid metabolism predominantly affecting muscle. The low incidence and lethal properties of this disease make anesthesia experience limited in such patients. Among all etiologies of LSMs, primary carnitine deficiency (PCD) is now considered highly treatable by early administration of L-carnitine, though it remains unclear whether L-carnitine is effective enough to protect diseased muscle against conventionally used neuromuscular blocking agents (NMBAs) during general anesthesia. Currently, no data are available concerning possible prolonged muscle weakness in these cases. Patient concerns: This case presents a 43-year-old female who was diagnosed with a PCD-induced LSM 3 years ago due to fatigability and exertional myalgias and has been treated with L-carnitine ever since. At the time of this report, she was admitted for uterine fibroids and scheduled for selective open gynecologic surgery under general anesthesia. Diagnosis: The patient's diagnosis of PCD-induced LSM was based on the clinical features, muscle biopsy, and diminished organic cation/carnitine transporter 2 (OCTN2) transporter activity in the patient's skin fibroblasts. Interventions: L-carnitine was taken by the patient until the morning of surgery. General anesthesia with cisatracurium and sevoflurane was selected as the anesthetic plan during the operation. The train-of-four (TOF) test was adopted as additional monitoring, particularly to track the recovery of neuromuscular function. Outcomes: The patient was extubated successfully following a spontaneously restored TOF ratio (TOFR) of 0.9. Nonetheless, we recorded a prolonged efficacy of cisatracurium in the clinical duration and the recovery time with TOFRs of 0.7 and 0.9, respectively. Lessons: The conventional dose of cisatracurium combined with a low dose of sevoflurane can be safely used in patients with LSMs without additional anesthetic risks. Meanwhile, continuous TOF monitoring is recommended to perform high-quality anesthesia.