Background and Objectives: Smear layer forms during cleaning and shaping can obstruct the entry of both irrigant and sealant into the dentinal tubules, resulting in the accumulation of the bacteria and their byproducts. To ensure effective adhesion and better periapical healing, it is strongly advised to remove the smear layer before proceeding with root canal obturation. This study was designed to compare the efficiency of laser-activated irrigation (LAI) in removing the smear layer and debriding the most apical third of the root canal. Materials and Methods: Sixty-five extracted human teeth with straight single roots were randomly and equally divided into four laser and one control groups. Root canals in all samples were shaped using prime size TruNatomy rotary files. During preparation, each canal was irrigated with 3 mL of 3% NaOCl and 3 mL of 17% EDTA alternately, followed by the irrigation with 10 mL of distilled water to avoid the prolonged effect of EDTA and NaOCl solutions. Final irrigation of 5 mL of 17% EDTA of the root canal was done to eliminate the smear layer and was subsequently activated by an endodontic ultrasonic tip for 20 s three times (control group), a flat-end laser tip (test groups 1 and 3) or a taper-end laser tip (test groups 2 and 4) for two cycles. The time of each cycle activation was 10 s (groups 1 and 2) or 20 s (groups 3 and 4) in which the Er:YAG laser of 2940 nm was used. The laser operating parameters were 15 Hz and 50 μs pulse duration. The samples were then split longitudinally and subjected to scanning electron microscopy (SEM). Results: The remaining smear layer at the apical part of the root canals was statistically significant between the control group and the laser groups 1 (p = 0.040) and 2 (p = 0.000). Within the laser groups, the exposed tubules count was greater in the laser with the flat tip as compared with the tapered tip (Laser 1 > Laser 2 and Laser 3 > Laser 4). Finally, no significant differences in the count of debris between the laser groups and control group were observed, except for laser 4 (p < 0.05), which had the highest count of debris. Conclusion: LAI to remove debris and smear layer at the apical third of the root canal is inferior to the current ultrasonic technique. However, when using the Er:YAG LAI, it is recommended to use a flat tip design for 10 sec for two cycles to ensure maximum debridement of the apical dentin surface.