Aim: To determine and compare the clinical and cost-effectiveness (CE) of Allium Sativum oil (ASO) versus Mineral trioxide aggregate (MTA) in primary molars pulpotomy in a group of Egyptian children. Methodology: This is a randomised clinical pilot study with two arms, parallel groups, and allocation blinded. Twenty-six children (n=52) participated in this clinical trial with maxillary and mandibular second primary molars indicated for vital pulpotomy and were randomly allocated into two equal groups. Group (I): pulpotomy using ASO, and Group (II): using MTA as pulpotomy agents. The follow-up period was one year, and the primary outcome was evaluating clinical effectiveness for both groups through the help of predetermined criteria during the follow-up period and according to the participant timeline. The secondary outcome was CE, measured using incremental CE ratio (ICER) and average CE ratio (ACER). Results: The relative risk of radiographic failure signs of the ASO group over the MTA group was (1.3) (95% CI 0.89:1.7) after 12 months. MTA had a higher (ACER) (67.00) than ASO (39.55). Conclusions: Allium Sativum oil is non-inferior to Mineral trioxide aggregate regarding clinical efficacy. ASO has a lower average cost-effectiveness ratio than MTA.