Background: The endoscopic modified Lothrop procedure (EMLP) is a common procedure performed in patients with frontal sinus pathology. While performing this procedure, large segments of bone are exposed, which may lead to the promotion of frontal sinus neo-ostium stenosis. Here we examine the peri-operative differences in time to achieve healing in patients where a mucosal flap is used to cover the exposed bone on one side of the neo-ostium. Design: A randomised pilot study with 12 patients undergoing EMLP surgery participated in this study. Methods: Patients were randomised to undergo a mucosal flap on either the left or right side of the neo-ostium. Prior to surgery, patients completed a SNOT-22 and smell identification test. Patients were reviewed until the neo-ostium had healed on both sides. Once healing had occurred, a post-operative SNOT-22 score and smell identification test were recorded. Results: Average time to healing for the frontal sinus neo-ostium was 4.7 vs. 4.2 (p = 0.3) on the flap vs. non-flap side, respectively. There was an average 24.4 point (range: −75 to +9) decrease in SNOT-22 scores post-surgery. The post-operative USPIT score demonstrated an average increase of 6.6 points (range −13 to +27). Conclusion: We did not detect significant differences in peri-operative time toward healing in neo-ostiums where a single flap is utilised. Further studies are needed to determine whether the usage of a single neo-ostium flap affords any benefit over no flap on either ostium. SNOT-22 and UPSIT scores improved post-surgery.