Background Surgical removal of impacted mandibular third molar is one of the most frequently performed interventions in oral and maxillofacial surgery. Objectives To compare two different flap designs in terms of sequelae and quality of life following surgical removal of impacted third molars. Methods This prospective, randomised, split-mouth clinical study involved patients referred for surgical removal of bilateral symmetrical impacted mandibular third molars. Envelope flap and modified triangular flap techniques were used. The effects of flap design on trismus, swelling, wound dehiscence, alveolar osteitis, haematoma, infection and quality of life were evaluated on post-operative days 3 and 7. Pain levels were assessed on post-operative days 1, 3 and 7. Results Significant differences were determined between the two groups in terms of trismus, pain and wound dehiscence scores on post-operative day 3. However, on post-operative day 7, this difference was observed only in trismus. Statistically significant differences were also determined between the two groups on post-operative day 3 for social isolation and eating subscale scores as well as total quality of life score. Conclusion Based on the study findings, the modified triangular flap may be superior to the envelope flap in terms of pain, trismus, and wound dehiscence in the first 3 days after impacted third molar surgery and may have a better impact on quality of life during this process.