Abstract Objectives To follow-up the situation of stunting among children in Nangapanda, a subdistrict in East Nusa Tenggara, Indonesia after 5 years. Methods The design was 5-year follow-up study in rural area of Indonesia. A total of 89 children aged 6–9 years were included. Structured interview, nutritional assessment, blood and stool collection were performed to the subjects who had the same measurement in 2014. Socio-demography characteristics, weight, height, hemoglobin level, serum ferritin, serum zinc, CRP, worm infection and household food security were collected. To compare the baseline and 5-year follow-up data wilcoxon test, paired t-test, and Mc-Nemar test were used. Results After 5 years, stunting prevalence dropped considerably from 49.4% to 21.3%. There were 34.1% children remain stunted after 5 years. Among the stunted children, 80% remained underweight, 33.3% remained anemia, and 16.7% still had worm infection. According to sociodemographic data, those who remain stunted had low mother's education (66%), lived with 5–8 household members (53.3%), experienced household food insecurity (53.3%), and consumed unsafe drinking water (46.7%). Compared to their nutritional status in 2014, there are improvements in their HAZ-score and hemoglobin level (P < 0.0001). In addition, worm infection rate reduced although the reduction was not significant (P = 0.077). Children whose HAZ-score improved were comparable in their sociodemographic status with those children who remained stunted children. Conclusions Within five year period, there was reduction in stunting prevalence which was accompanied by increase in HAZ-score, hemoglobin level and reduction in worm infection rate. No difference was found in characteristics of children who recovered and remained stunted. Funding Sources Pintermidi Grant from Universitas Indonesia with contract number 1908/UN2.R3.1/HKP.05.00/2019.