This study aims to investigate the connection between conditional cash transfers (CCTs) and stunting and identify the factors contributing to stunting among Indonesia’s poor. The analysis relies on the data collected in 2007 and 2009. Infants aged 0–36 months from families receiving CCTs were compared with a control group using the randomized controlled trial (RCT) method. These infants from poor households, who were stunted, and were not exclusively breastfed, were selected randomly. The data were analyzed using logistic regression with the STATA program (v.13). The research findings show that CCTs alone can not impact the prevalence of stunting. In order to optimize the effectiveness of the CCT scheme, factors related to the mother’s age at childbirth, education, employment, the sex of the household head, and the geographic condition should be taken into account. This research would reinforce the need for CCT programs linked closely in design with effective social behavior change programs. The study recommends further research examining how CCT would impact stunting among groups in low-income families.