Introduction: Salivary melatonin is a critical antioxidant that contributes to oral health by mitigating oxidative stress. Psychological stress linked to thumb sucking may disrupt oral homeostasis, leading to conditions such as dental caries and fungal infections. Aim: This study explores the relationships between thumb sucking, salivary melatonin levels, dental caries, and the presence of Candida albicans (CA) in children. Materials and methods: A case-control study was conducted with 60 children aged 4-5 years at the University of Baghdad’s College of Dentistry. Participants were divided into thumb-sucking (n=30) and non-thumb-sucking (n=30) groups. Salivary melatonin levels were measured using enzyme-linked immunosorbent assays (ELISA), dental caries were assessed via the dmfs index, and CA counts were quantified on Sabouraud dextrose agar (SDA). Statistical analyses were performed, including t-tests, ANOVA, and correlation assessments. Results: Thumb-sucking children exhibited significantly lower salivary melatonin levels (28.620±2.278 pg/mL) compared to controls (34.525±2.142 pg/mL; p=0.044). The thumb-sucking group also had higher dmfs scores (15.033±1.449 vs. 8.667±0.899; p=0.000) and greater CA counts (18.900±1.048 vs. 13.583±0.549; p=0.000). Negative correlations were observed between salivary melatonin levels and the severity of dental caries, while positive correlations linked CA with dental caries. Conclusions: Thumb sucking adversely affects pediatric oral health by reducing salivary melatonin, increasing dental caries risk, and promoting fungal overgrowth. Early intervention to curb thumb-sucking behaviors may mitigate these risks and improve oral health outcomes.