Rotavirus infection is the leading cause of acute diarrhea in children and is preventable with a vaccine. Malnutrition increases the risk for the development of enteric and respiratory diseases, but also diarrhea increases the risk for stunting, having a negative effect in height-for-age Z score (HAZ). Therefore, Rotavirus can be considered as one of the contributing factors to stunting. The objective was to determine if vaccination against rotavirus was associated with changes in HAZ of children aged 6–60 months. We analyzed the data of Demographic and Health Survey (DHS) 2015–2017 for Peru, which is a nationwide representative. We fitted linear regression models controlling for complex sampling. The vaccine coverage was close to 75.5%, and the mean HAZ was −0.76 standard deviations. After adjusting by demographic, health, and household characteristics, children who received rotavirus vaccine, had a mean HAZ 0.06 standard deviations higher than children who did not receive it. Additionally, BCG vaccination, a higher education level of the mother, a higher wealth index, and treating water for drinking were positively associated with HAZ. On the other hand, we found low birth weight, lack of flush toilet, and altitude higher than 2500 m above sea level negatively associated with HAZ. Rotavirus vaccine is associated with better anthropometric measurements.