Background and aim: To establish lesion sterilization and tissue repair (LSTR) therapy as an alternate treatment option in managing infected primary molars with poor prognosis that were indicated for extraction, thereby fulfilling the objective of retaining the primary tooth till its normal exfoliation in the dental arch. Materials and methods: A total of 84 children who met the inclusion criteria requiring extraction in 142 teeth involving primary molars were included in the study. The selected patients were allocated to two groups, that is, group I—LSTR therapy with 3Mix-MP paste and group II—pulpectomy with metapex. All the treated teeth were then clinically and radiographically evaluated after 1, 3, 6, 9, and 12 months, respectively, to determine the success between groups I and II. Pearson's Chi-squared test along with the z-test was used to compare the clinical and radiographic success of the two groups (p < 0.05). Results: Pain and tenderness were completely resolved within one month of follow-up in both groups. Abscesses were resolved completely at 1 month in the pulpectomy group and mobility was resolved at 6 months follow-up in both groups. Interradicular and periradicular radiolucency persisted even at 12 months of the follow-up period in both groups. The intergroup comparison revealed no statistical differences between LSTR and pulpectomy procedure and both were equally effective at all time intervals (p > 0.05). Conclusion: Both LSTR therapy with 3Mix-MP and pulpectomy with metapex showed 100% clinical success rates. Radiographically no changes were observed even at the 12-month follow-up period in both groups. LSTR therapy can be an alternative treatment option for pulpally involved primary teeth with poor prognosis and in cases where mechanical instrumentation could not be achieved due to physiologic root resorption.