Alveolar Osteitis (AO) is a complication occurs on the post-extraction days that includes pain and disintegrated blood clot. Chlorhexidine (CHX) rinse after extraction is an effective method for decreasing the incidence of AO. Honey has natural antibacterial properties and effectiveness when it is used as a dressing on burns and wounds. However, the effect of intraoral honey dressings on healing is still not adequately studied. This study aimed to compare pain and AO after extraction of a molar tooth in a group of patients who received the intra-alveolar application of Manuka Honey post-operatively with another group who used 0.2% CHX rinse. A randomized clinical trial of parallel groups was carried out on 100 patients who had a single molar tooth extraction. They were randomly divided into two groups. Group1 (G1) used 0.2 % CHX twice daily for 7 days. In Group2 (G2), Manuka Honey applied topically by a cotton swab into the socket directly after extraction and on Day3. Re-evaluation, including pain assessment, empty socket, and halitosis was done on day 3 and day 7. G1 included 43 patients and G2 included 57 patients. Higher grades of pain, more empty sockets, and halitosis were found in G2 than in G1 on day3 and day7 without significant differences. Four cases of AO were found in G1 (9.3%) and 7 cases in G2 (12.3%), without significant difference between the two groups according to Chi-squared tests (p=0.753). The application of Manuka honey in the extraction socket directly after extraction and on day 3 has been found to be insignificantly less efficient in the prevention of AO than CHX rinse twice daily for seven days. However, honey is promising as natural dressing material and further studies are recommended.