Aim: To evaluate the penetration depth of irrigants into root dentin after manual, ultrasonic, and sonic activation using the dye penetration method under light microscope. Materials and methods: Ninety-two extracted single-rooted human teeth were used in the age range of 14–18 years. After access opening, root canals were instrumented. Canals were irrigated with preheated 5% sodium hypochlorite (NaOCl). Teeth were divided into four groups—group I, control group without activation; group II, manual dynamic activation; group III, ultrasonic activation; and group IV, sonic activation. About 1% methylene blue dye was used, which was activated for 30 seconds using the respective activation method. Cross sections of apical 1 mm were prepared from the apical third. Each section was examined under a light microscope to check the penetration depth of dye in a micrometer at the apical third level. Results: There was a statistically highly significant difference seen for the values between the groups (p < 0.01) with higher values in group IV and least in group I, revealing that group IV had higher penetration depth compared to other groups. Conclusion: The use of needle irrigation with the use of EndoActivator (sonic agitation method) has enhanced irrigation in the apical third. Clinical significance: As during biomechanical preparation and irrigation with the traditional method of needle and syringe, canals remain inadequately disinfected at the apical third level. So, this study was done to assess whether the advanced methods of activation are more effective than commonly used techniques in their ability to penetrate dentinal tubules.