Background: Dental caries remains a highly prevalent chronic disease in children, with occlusal surfaces of primary molarsparticularly susceptible due to complex pit and fissure morphology. Pit and fissure sealants are effective preventive measures, but comparative long-term performance of resin-based sealants (RBS) and resin-modified glass ionomer cement (RMGIC) for cavitated dentine lesions in primary molars remains unclear. Objective: To compare the long-term clinical performance, retention, and patient experience of RBS versus RMGIC in the management of occlusal cavitated dentine caries with limited extension in primary molars. Methodology: A randomized, non-blinded split-mouth clinical study was conducted on 70 children with matched primary molars. One tooth per child received RBS and the contralateral tooth RMGIC. Treatments were performed without rubber dam using standard moisture control. Clinical evaluations were conducted at 3, 6, 12, 24, and 36 months. Defect-free survival, dentist- and child-reported experiences, and correlation with treatment variables were assessed. Statistical analysis included McNemar test, Wilcoxon Signed Rank test, and Spearman correlation (p < 0.05). Results: At 36 months, RMGIC demonstrated higher accumulated defect-free retention than RBS (85.7% vs. 71.4%), with significant superiority at 24 months (94.3% vs. 71.4%, p = 0.0005). Dentist-rated child experience and cooperation correlated positively with RMGIC success, while RBS outcomes were independent of behavioral variables. No significant difference was observed in child-reported experience or dental fear scores. Conclusion: RMGIC provides superior long-term clinical performance and accumulated success in primary molars with limited occlusal cavitated dentine caries, especially in cases with suboptimal isolation. RBS remains suitable where ideal moisture control is achievable.