Background: Tribal children in India bear a higher burden of undernutrition when compared to other communities. However, inequality within tribal communities is under-researched. Objectives: To examine the factors associated with inequality in undernutrition between Paniya and Kurichiya tribal communities in Wayanad district of Kerala. Methods: A cross-sectional analytical study was conducted during August to October 2018 among 314 children aged 2-5 years belonging to Paniya (151) and Kurichiya (163) communities. Participants were selected using multistage cluster sampling. Data were collected using structured interview schedule based on household food insecurity access scale; relevant individual, parental, and household factors were ascertained; child nutritional status was assessed based on anthropometric measurements. The composite index of anthropometric failure (CIAF) was used as an aggregate indicator of undernutrition. Statistical analysis was done using Chi-square test and univariate and multivariable logistic regression. Results: There were significant differences in the prevalence of stunting, underweight, and wasting between Paniya (52.3%, 58.9%, and 25.2%, respectively) and Kurichiya (28.2%, 31.1%, and 12.3%, respectively) tribal children. Based on the CIAF, 66.9% and 41.1% of Paniya and Kurichiya children, respectively, were undernourished. Intratribal difference was observed to exist in all three forms of anthropometric failures simultaneously. Significant factors associated with CIAF were community identity, household food insecurity, and maternal early marriage. Significant factor associated with all three forms of undernutrition was maternal experience of domestic violence. Conclusion: This study demonstrates the child nutritional inequality within the tribal communities and indicates the need for more focused policies and programs among vulnerable tribal groups to ensure food security and empowerment of women.