The aim of this study was to compare the post-operative sequelae of removal of impacted third molars in participants treated with conventional flap elevation technique or with a minimally invasive flapless technique. Participants with bilaterally impacted mandibular third molars were included. They were divided into two sites constituting 2 groups. One group was operated by using conventional flap design and elevation and other with flapless technique. Objective clinical parameters were recorded and compared in the post-operative period like mouth opening, swelling, surgical time, and pocket depth. Subjective parameters including pain were also assessed and statistically analyzed. The sites operated in Group II (Flapless technique) had better results (p≤0.05) in terms of pain, swelling, trismus, and pocket depth distal to second molar when compared to Group I (Flap). The flapless technique gives better surgical results and improved healing process after third molar removal and so should be recommended in routine clinical practice.