Objectives: Although there are different ways of performing medial branch neurotomy on facetogenic low back pain, few studies have compared clinical outcomes of a parallel technique over the medial branch vs. a perpendicular technique. We investigated differences in pain outcome with both techniques. Design: This was a prospective, pilot, randomized, pragmatic trial (double blinded in the diagnostic phase). Setting: A comparative pilot trial was conducted at an academic pain center. Methods: Patients who did not respond to conservative medications and had severe lumbar pain for more than 3 months (VAS score ≥ 65) were included. A double diagnostic block with local anesthetic and placebo was performed, double blinded. Patients who had 80% relief from the local anesthetic and no substantial relief from placebo were randomized to undergo medial branch neurotomy under fluoroscopy, placing an electrode parallel or perpendicular to the medial branch. The primary outcome was differences in the VAS score at 1, 3, and 6 months. The secondary outcomes were Oswestry Disability Index score, Roland Morris Questionnaire score, and other functional Likert scale scores. Results: Forty-three consecutive patients were randomized to parallel (n = 20) or perpendicular (n = 23) neurotomy. There were no significant differences in VAS, Oswestry Disability Index, or Roland Morris Questionnaire scores at 1, 3, or 6 months between groups. Statistically significant differences were found in the categorical analysis at 6 months in the evolution of pain, Oswestry Disability Index score, Roland Morris Questionnaire score, and some Likert scale scores in favor of the parallel group. Conclusions: There were differences at 6 months in the categorical analysis of the evolution of pain, Oswestry Disability Index score, Roland Morris Questionnaire score, and some functional Likert scale scores, all in favor of the parallel group. &