Aim: The aim of this study is to evaluate the postoperative pain of mineral trioxide aggregate (MTA) and propolis after pulpotomy in carious lower primary molars. Methodology: 28 Healthy children aging 5-8 years old with at least one carious primary molar at each side. Each child received MTA in right or left side and Propolis in the other side. Clinical follow up was done at 3, 6, and 9 months. Radiographic follow up was done at 6 and 9 months. Results: All cases were free of pain along the follow up period except one case in propolis group showed pain after 6 months then disappeared at 9 months. Sinus tract appeared in 3.85% in propolis group at 6 months and 4% in both groups at 9 months. Regarding periapical radiolucency, in MTA group, 3 cases (11.54%) were affected after 6 months and 4 cases (16%) after 9 months. In propolis, 4 (15.38%) of cases were affected after 6 months, and 6 (24%) of cases after 9 months. Furcation Involvement, appeared in MTA group, in 2 (7.69%) cases were affected after 6 months. While in propolis group, 6 (23.08%) cases were affected after 6 months. Conclusions: The clinical outcome of propolis is comparable to that of MTA at both 6 and 9 months follow up period. On the other hand, MTA showed better results in all radiographic outcomes when compared to propolis.