BACKGROUND: We investigated the efficacy and safety of thread-embedding acupuncture (TEA) for chronic low back pain (LBP) in a randomized controlled pilot trial with the aim of laying the foundation for a large-scale randomized controlled trial on this topic. METHODS: Forty participants were recruited for this two-arm, assessor-blinded randomized controlled pilot trial. The participants were randomly allocated to a TEA group (experimental group) or an acupuncture group (control group). The TEA group received TEA once every 2 weeks for 8 weeks (four sessions in total), while the acupuncture group received acupuncture twice per week for 8 weeks (16 sessions in total). The primary outcome was the visual analog scale (VAS) score for pain and the secondary outcomes were short-form McGill Pain Questionnaire (SF-MPQ) and Oswestry Disability Index (ODI) scores. Assessments were performed at screening and at 2, 4, 6, 8, and 10 weeks after treatment initiation (the 10-week assessment was conducted at 2 weeks after treatment cessation). RESULTS: Of the 40 participants, 36 completed the study and four dropped out. Both the TEA group and the acupuncture group showed significant improvements in VAS, SF-MPQ, and ODI scores in a time-dependent manner. Furthermore, with regard to ODI, a significant interaction between group and time was observed, with the two groups exhibiting a different pattern of change at 8 weeks according to contrast analysis with Bonferroni's correction. No serious adverse event occurred, and hematological and biochemical test findings were within normal limits. CONCLUSION: This pilot study has provided basic data for a larger clinical trial to demonstrate the efficacy and safety of TEA for chronic LBP. TRIAL REGISTRATION: Clinical Research Information Service of the Korea National Institute of Health, ID: KCT0001819 . Registered on 15 February 2016.