Objective (1) This trial will compare the clinical and psychosocial effectiveness of in-group and individually pain neuroscience education (PNE) in patients with chronic low back pain (CLBP). In addition, (2) the influence of social determinants of health on post-treatment results will be analyzed. Methods A three-arm randomized controlled trial will be conducted. Sixty-nine participants with CLBP will be recruited in a 1:1:1 ratio. Participants, assessor, and statistician will be blinded to group assignment. The PNE intervention will be adapted to the context of the participants. An experimental group (n = 33) will receive PNE in an in-group modality, the other experimental group (n = 33) will receive PNE in an individually modality and the control group (n = 33) will continue with usual care. Additionally, participants will be encouraged to stay active by walking for 20–30 min 3–5 times per week and will be taught an exercise to improve transversus abdominis activation (bracing or abdominal following). The outcome measures will be fear avoidance and beliefs, pressure pain threshold, pain self-efficacy, catastrophizing, pain intensity, and treatment expectation. Outcome measures will be collected at one-week before intervention, immediately post-intervention, and four-weeks post-intervention. Conclusion The innovative approach of PNE oriented to fear beliefs proposed in this study could broaden the application strategies of this educational therapeutic modality. Impact. Contextualized PNE delivered by physical therapist could be essential to achieve a good cost-effectiveness ratio of this intervention to improve the clinical condition of people with CLBP.