Topical applications of emollients such as sunflower seed oil and Aquaphor have been shown to reduce the incidence of bloodstream infections and mortality of preterm infants in resource-poor settings. The causal mechanism for prevention of infection through cutaneous portals of entry is not well understood. We examined the relationship between skin condition score as a measure of skin barrier integrity and risk for bloodstream infection, and the effect of emollients on that relationship. Data for this study come from a randomized controlled trial of the impact of topical emollient therapy on nosocomial infections in 491 preterm infants <33 weeks gestational age at Dhaka Shishu Hospital, Bangladesh. Latent growth trajectory model with random-coefficient and multivariable logistic regression were utilized. Rate of deterioration of skin condition was significantly lower (P < 0.05) in both emollient arms compared with the untreated control group. Adjusted odds ratio of skin score for infection was 1.32 (95% confidence interval: 1.06-1.65). Emollients reduced the incidence of infection only when the skin had no signs of deterioration Aquaphor incidence rate ratio: 0.43 (95% confidence interval: 0.19-0.97) and sunflower seed oil incidence rate ratio: 0.46 (95% confidence interval: 0.21-0.99). Skin condition deteriorated progressively after birth and compromised skin condition increased the risk of infection. Emollients preserved skin integrity and thus prevented infection in preterm neonates. To optimize benefits of emollients for the prevention of bloodstream infection, use of emollients should begin immediately after birth when the skin is still intact.