The physical growth and cognitive development of elementary school children are very crucial and this group is large in number but has little research dedicated to it. The physical growth and cognitive development of children occur simultaneously and can be measured by body mass index (BMI) and intelligence quotient (IQ). Previous studies could not sufficiently focus on both aspects. The aim of this study was to identify determinants of BMI and IQ of students in two elementary schools in the Humla district of Nepal. Two randomly selected elementary schools and all children available there (n
= 173) participated in the study. BMI was calculated with the objective of proper measurement of height and weight of the children. Likewise, the updated universal nonverbal intelligence test (UNIT) was applied for IQ. Descriptive statistics, t
-test, analysis of variance and multiple linear regressions were used when appropriate. Study findings showed that one-tenth of the children had grade 2 thinness (-2SD) and about one-third had poor IQ (<85). The age of the children (p
< 0.05) and household economic status (p
< 0.001) were significant for the BMI. Likewise, frequencies of illness in the previous year, mother’s education (p
< 0.05) and father’s education (p
< 0.001) were significant factors for the IQ score. More commonly, BMI and IQ scores were significantly lower in the ultra-poor group. Economic status and parent education are still major determinants of IQ and BMI in these students. Special programs and strategies should be launched to improve the poor ranking of IQ and BMI.