To compare the clinical and radiographic outcomes of Pulpotomy in Primary molars using Protooth Cement and MTA. Materials and Methods: 20 patients with an age range of 5–9 years with 40 bilaterally symmetrical primary molars that had deep carious lesions were incorporated into a randomized split mouth clinical trial. Initially, the caries was removed. Afterward, the teeth randomly underwent pulpotomy with either MTA or Protooth. The pulp chambers of both the groups will be restored with GIC followed by SSC placement. The teeth will be evaluated at 1, 3, & 6 months periodically to assess the clinical and radiographic outcomes. Results: Statistical analysis was done using SPSS version 25.0. P value < 0.05 was considered statistically significant. At the end of 6 months the clinical and radiographic success rate of group A was 96.4 and 96.4% respectively which was comparable with group B which showed a success of 98.3% clinically and 100% radiographically. Statistically, there was no significant difference between both the groups. Conclusion: Results from the study suggest that “Protooth” can successfully be used as an alternative pulpotomy medicament in deciduous molars. However, further clinical trials with longer follow up periods and larger sample sizes are recommended for better results.