Aim: To compare the efficacy of casein phosphopeptide-amorphous calcium phosphate (CPP-ACP) (GC Tooth Mousse) and tricalcium phosphate formulation (Clinpro) by topical application and iontophoresis. Background: Noninvasive treatment of dental caries is a major advance in the clinical management of the disease. Materials and methods: A total of 20 primary anterior and 20 primary molars were included in the study to be analyzed by transverse microradiography (TMR) and polarized light microscopy (PLM). The samples were coated with acid-resistant varnish, leaving a window on the buccal/lingual surface of enamel and immersed in demineralizing solution for 96 hours. Each sample was coated with varnish on the left half (control), and the right half served as a test. All the samples were divided into four groups. The test windows of specimens in groups I (GC Tooth Mousse) and II (Clinpro) were subjected to remineralization treatments for 10 days. Similarly, groups III and IV were subjected to iontophoresis using GC Tooth Mousse and Clinpro for 7 minutes. The samples were analyzed by TMR and PLM. Results: There was no significant difference in the mean difference of mineral loss among the four groups. There was a significant difference in the mean difference of lesion depth among the four groups. Conclusion: Both iontophoresis and topical application were equally efficient, but one remineralization by iontophoresis equals 10 topical applications.