Background and Aim: Due to the increasing use of proton pump inhibitors (PPIs) and their side effects for bone repair and the high percentage of therapy failure in lumbar fusion surgery, especially in various animal studies, the goal of this study was to appraise the consequence of pantoprazole and famotidine on new bone formation in patients experiencing spinal fusion surgery. Methods and Materials/Patients: In this double-blind clinical trial, eighty patients participated based on the inclusion and exclusion criteria, of whom 40 cases received pantoprazole (group P) and 40 received famotidine (group F) for eight weeks. They were followed up for three, six, and twelve months after surgery for cage subsidence, screw loosening, and visual analogue scale (VAS), Oswestry disability index (ODI), Brantigan, Steffee, Fraser (BSF), and Lenke classification for grading their bone formation. A P<0.05 was considered significant. Results: The rate of fusion based on the Lenke score was lower in the group receiving pantoprazole six and 12 months after the surgery compared to group F (the frequency of Lenke grades C and D were 35% and 25% compared to the famotidine group 12.5% and 12.5%, respectively; P=0.042). The VAS Mean±SD score in group F was lower than group P after 12 months (2.48±1.06 and 1.83±0.55, respectively; P=0.008). There was no pharmacologically significant association between subsidence (P=0.43), loosening (P=0.13), ODI (P=0.31), and BSF (P=0.77) 3, 6 and 12 months post-operation. Conclusion: Affording to the preliminary conclusions of this study, the use of pump inhibitors, such as pantoprazole is more destructive for the ossification process in candidates for spinal fusion requiring the chronic use of drugs for controlling their gastric acid secretion, and H2-blocking drugs, such as famotidine are preferable in this situation after further investigations.