From 2005 to 2017, the prevalence of mortality in Vietnamese children under five years old showed large regional disparities. In 2017, mortality in the wealthiest region was 12.6‰, whereas the most disadvantaged region it was three times as high, at 36‰. This study aims to identify factors affecting regional disparities of the under-five mortality rate (U5MR) in Vietnam. We applied Structural Equation Modelling to estimate the degree and the pathway through which undernutrition and socio-economic status (SES) contributed to the under-five mortality disparities. SES is estimated as a common latent factor of three socio-economic measures, that is, education, poverty and income. The direct effect of SES on U5MR is at 2.16 through the underweight pathway, which is 5 times higher than the effect of underweight on U5MR. Through the stunting channel, this direct impact is 1.43, nearly twice as high as the impact of the stunting rate. SES also has an indirect effect on U5MR through these undernutrition pathways. In total, we estimate that an increase in SES index will make the U5MR increase by 2.73‰. Among the three indicators of SES, poverty conveys the strongest signal of a considerable change in SES, thus to a subsequent change in U5MR. Among two types of undernutrition, the effect of stunting on U5MR is dominant, more than 3 times as high as that of underweight. These findings have important implications for socio-economic and health interventions: those that strongly focus on the reduction of regional poverty and stunting rates would be effective in bridging the regional gap in the U5MR in Vietnam.