Objectives: To clinically and radiographically compare the outcomes of pulpotomy with mineral trioxide aggregate (MTA) and human amniotic membrane (HAM) in primary molar teeth at 1, 3, 6, and 12 months. Materials and methods: The study was a randomized clinical trial with two arms. One arm consisted of participants whose pulpotomy was conducted using MTA, called group I, and the other arm, using HAM, was designated group II. Results: Both MTA and HAM exhibited 100% clinical success. Also, there were no signs of external resorption, periapical bone destruction, or internal resorption in both the MTA and the HAM groups at all four time intervals in this study. However, periodontal ligament widening was seen in 30% of the participants in the MTA group at 1-month and at the 12-month follow-up, whereas in the HAM group, periodontal ligament widening was found to reduce significantly from 22.2% at 1-month to 11.1% at the 12-month follow-up. Conclusion: The HAM exhibited favorable clinical and radiographic outcomes in the present study. Clinical significance: Mineral trioxide aggregate is the most preferred choice as a pulpotomy agent for deciduous teeth. However, various drawbacks associated with MTA have been fueling the need for newer, effective agents. HAM is not only easily available, cost-effective, and easy to handle but also favors tissue regeneration. The positive outcome of the present study strongly advocates the use of HAM as an alternative to MTA for pulpotomy in primary teeth.