Purpose: The current trial sought to assess the intensity of post-operative pain following endodontic instrumentation of first mandibular molar teeth with Fanta (Pepsi gold) (FPG) and M3-pro+ Gold (assorted) (MPG) rotary files. Methods: In a randomized; single-blind clinical trial, 40 asymptomatic first mandibular molars with irreversible pulpitis, normal periapical radiography, and a need for conventional endodontic treatment were offered treatment. It was registered under NCT06382545. The participants were randomly distributed into two groups (n=20) based on the file system utilized. The chemo-mechanical preparation was done in one session. Patients were requested to rate their post-instrumentation pain on a visual analogue scale (VAS) at 12, 24, and 48 hours, (no discomfort, mild pain, moderate pain, and severe pain). Results: Following three time periods, the FPG group scored a higher VAS rating than the MPG group. The highest VAS value in both groups was achieved at 12 hours, although it decreased significantly after 24 and 48 hours. Conclusion: Post-instrumentation pain is common following the preparation of the root canal system using the FPG and MPG rotary systems tested, however it only lasts a short time. Although more common after utilising the Pepsi gold system, the majority of cases reported minimal discomfort at all time points.