Introduction: Visualizing the pulp cavity requires adequate knowledge of the size, morphology, and variation of the root canals of primary teeth. The morphology of the root canals in deciduous teeth causes difficulties during endodontic treatment. There have not been many studies on root canal variations in primary teeth in the Indian population. Aim and objective: To assess the variation in the root and canal morphology of primary maxillary second molars using cone-beam computed tomography (CBCT) in the pediatric Indian population. Materials and methods: The institutional database and private diagnostic centers were used to gather CBCT images of 25 children (50 images) between the age-group of 5 years and 9 years. The CBCT images were rebuilt using Scanora software, and the data were assessed and analyzed using the SPSS version for Windows. Results: Out of 50 primary maxillary second molars, the majority of the second molars had three roots and three canals (Variant I) which account for 66% of teeth. Variant II had three roots and three canals with distobuccal and palatal roots fused in 14% of cases whereas 18% of cases showed three roots and four canals in which mesiobuccal root had two canals (Variant III). The remaining 2% of cases showed four roots with four canals (Variant IV) which were statistically significant. Conclusion: We concluded that within the constraints of our study, there was a difference in the root canal configuration of primary maxillary second molars in the investigated group of the Indian population.