Introduction: post endodontic pain comprises a consequence to root canal treatment as it is an unpleasant outcome to both patient and the clinician. Aim of this study : to compare the level of post endodontic pain after instrumentation with ProTaper Gold or KontrolFlex systems. Methodology: 70 patients were randomly allocated to two groups 35 patients each. Group A: canals were instrumented using ProTaper Gold system, Group B: canals were instrumented using KontrolFlex system. Patients were asked to record their pain levels after 6h, 12h, 24h and 48h using the visual analogue scale. Data were tabulated and statistically analyzed using Shapiro Wilk test and Kolmogrov Smirnov test. Results: ProTaper Gold was associated with significantly less pain after 6h and 12h after which no statistically significant difference was found. Conclusion: There was a statistically significant difference in the post endodontic pain after 6h and 12h after which no statistically significant difference was found. The pain steadily decreased over time in both systems.