Children living in the internally displaced person (IDP) camp are at higher risk of stunting. This cross-sectional study aimed to assess the prevalence and to identify the associated factors of stunting among children aged 6–59 months at Myaing-Gyi-Ngu IDP camp in Kayin State, Myanmar. According to the World Health Organization Child Growth Standards, children with a height-for-age Z-scores below −2 standard deviation of the reference median (HAZ ≤ −2) were classified as stunted. Multiple logistic regression analysis was performed to identify the strong predictors. Prevalence of stunting has been found very high (59.4%). Adjusted model revealed that children living with illiterate mothers (odds ratio [OR], 1.86; 95% confidence interval [CI], 1.07–3.24), being third/later-birth child (OR, 1.88; 95% CI, 1.13–3.14), consuming less than 4 food groups (OR, 4.22; 95% CI, 1.94–9.16), and older age of child (OR, 6.36 for 13–24 months; 95% CI, 2.74–14.74, 7.45 for 25–36 months; 95% CI, 3.21–17.25 and 12.75 for 37–59 months; 95% CI, 5.51–29.52) had higher odds of becoming stunted. The levels of support availability, presumed support and support received of mothers were generally low, but no significant associations were observed. In conclusion, this study showed high prevalence of stunting, but low dietary diversity and social support in the IDP camp. Due to the significant association of dietary diversity scores with stunting, interventions aiming at improving dietary diversity should be taken to reduce the stunting among children in the IDPs camp.