Aims: The purpose of the study was to assess the effect of nutrition on salivary flow rate (SFR) (unstimulated and stimulated), dental caries status, and eruption pattern in healthy and malnourished children. Materials and Methods: The study participants were categorized into healthy (Group I, n = 37) and malnourished groups (Group II: Malnourished height-for-age [n = 30] and Group III: Malnourished weight-for-age [n = 30]) as per classification of chronic malnutrition. SFR, dental caries status, and eruption pattern were noted for all groups. Statistical Analysis: Analysis of variance (ANOVA) was used to analyze the differences in unstimulated and stimulated SFR and dental caries among three groups. The lowest square difference was used for post hoc comparison and Pearson's correlation to investigate the association between SFR and dental caries. The statistical significance was set at P < 0.05. Results: The unstimulated SFR values were found to be 0.53 ± 0.15 ml/min (Group I), 0.14 ± 0.04 ml/min (Group II), and 0.21 ± 0.20 ml/min (Group III). For stimulated SFR, the values were 1.94 ± 0.44 ml/min (Group I), 1.17 ± 0.48 ml/min (Group II), and 1.07 ± 0.52 ml/min (Group III). Dental caries status was recorded to be 2.43 (Group I), 6.4 (Group II), and 4.66 (Group III). The participants with delayed eruption pattern were 8.10%, 23.30%, and 16.60% for Group I, Group II, and Group III, respectively. Conclusion: The values for unstimulated and stimulated SFR were significantly less, but dental caries status and delayed eruption were found to be more in malnourished groups as compared to the normal group.