Postnatal antiretroviral (ARV) prophylaxis for infants born to women with HIV is a critical component of perinatal HIV transmission prevention. However, variability in prophylaxis regimens remains and consistency with guidelines has not been evaluated in the United States. We evaluated trends over time in prophylaxis regimens among 6386 HIV-exposed uninfected (HEU) infants using pooled data spanning two decades from three US-based cohorts: the Women and Infants Transmission Study (WITS, 1990-2007), Pediatric AIDS Clinical Trials Group (PACTG) 219C (1993-2007), and the PHACS Surveillance Monitoring of ART Toxicities (SMARTT) study (2007-2015). We also identified maternal and infant risk factors for use of combination prophylaxis regimens (≥2 ARVs) and examined consistency with US perinatal guidelines. We found that receipt of combination prophylaxis between 1996 and 2015 ranged from 2% to 15%, with a consistent median duration of 6 weeks. Infants whose mothers had lower CD4 T-cell counts, higher viral load (VL), no antepartum ARVs, age <20 years at delivery, and Cesarean delivery had significantly higher rates of combination prophylaxis, while infants born 2006-2010 (vs. 2011-2015), who were Hispanic or with lower maternal education levels, had significantly lower rates. Predictors for combination prophylaxis varied over time, with the strongest associations of maternal VL in later birth cohorts. While use of combination prophylaxis increased over time, only 50% of high-risk infants received such regimens in 2011-2015. In conclusion, HEU infants at higher risk of HIV acquisition are more likely to receive combination neonatal prophylaxis, consistent with US guidelines. However, substantial variability remains, and infants at higher risk often fail to receive combination prophylaxis.