Background The extraction of third molars is one of the most common procedures in oral and maxillofacial surgery clinic. Surgical extraction involves the manipulation of both soft and hard tissues, so the patient usually experiences pain, swelling, and trismus in the immediate post-operative period. Several studies have been conducted using different types of surgical flaps to provide access with the least possible damage of soft tissues. Designing and implementing an optimum flap, which provides easier technique, better visibility, minimal post-operative complications, and best healing, is an aspired goal of every oral surgeon. This study aimed to compare lingual-based four-cornered flap with conventional triangular flap, and to evaluate its effect on post-operative pain after surgical extraction of impacted lower third molars. Material and Methods Seventeen patients (age ranged from 19 to 26 years) with bilateral, symmetrical impacted lower third molars (n=34) were included in the study. This was a randomized clinical trial with a split-mouth design. The impacted molars were assigned randomly, by coin flipping, to two groups: Case side with lingual-based four-cornered flap (Group A), and control side with conventional triangular flap (Group B). Away from the incision, the prognosis, surgical intervention, and postoperative procedures were exactly the same for the two groups. Postsurgical pain was assessed for 5 days using visual analogue scale (VAS) and by recording patients need for analgesics on a daily basis. Patients were also evaluated via a self-reporting questionnaire, i.e. Postoperative Symptoms Severity (PoSSe) scale, administered on the seventh postoperative day. Results Pain scores recorded in Group A were found to be significantly lower as compared to pain scores in Group B in the 5 postoperative days ( P <0.05). Total analgesic intake in Group B was significantly higher ( P <0.05). PoSSe scores were lower in Group A, however, this difference was insignificant ( P >0.05). Conclusions According to the data of the current study and within its limits, it appeared that lingual-based four-cornered flap design was superior to the conventional triangular flap regarding the postsurgical discomfort and pain. Key words: Impaction, third molar surgery, flap design, pain, PoSSe scale, split-mouth, RCT.