Prenatal drug exposure (PDE) is known to affect fetal brain development with documented long‐term consequences. Most studies of PDE effects on the brain are based on animal models. In this study, based on a large sample of 133 human neonates and leveraging a novel linear mixed‐effect model designed for intersubject variability analyses, we studied the effects of six prenatally exposed drugs (i.e., nicotine, alcohol, selective serotonin reuptake inhibitor, marijuana, cocaine, and opioids) on neonatal whole‐brain functional organization and compared them with five other critical nondrug variables (i.e., gestational age at birth/scan, sex, birth weight, and maternal depression). The behavioral implications were also examined. Magnitude‐wise, through summing across individual drug effects, our results highlighted ~5% of whole‐brain functional connections (FCs) affected by PDE, which was highly comparable with the combined effects of the five nond rug variables. Spatially, the detected PDE effects featured drug‐specific patterns with a common bias in higher‐order brain regions/networks. Regarding brain–behavioral relationships, the detected connections showing significant drug effects also demonstrated significant correlations with 3‐month behavioral outcomes. Further mediation analyses supported a mediation role of the detected brain FCs between PDE status and cognitive/language outcomes. Our findings of widespread, and spatially biased PDE effect patterns coupled with significant behavioral implications may hopefully stimulate more human‐based studies into effects of PDE on long‐term developmental outcomes.