Aflatoxin B1 (AFB1) a mycotoxin produced by Aspergillus flavus and A. parasiticus is a potent carcinogen and causative agent of hepatocellular carcinoma (HCC). It is a food contaminant which presents a major risk to human health. AFB1 contamination poses a significant economic burden, as 25% of the world's food crops need to be destroyed annually. The mechanism of action (MOA) of aflatoxins remains to be fully elucidated. An integrative systems biology approach was therefore undertaken to decipher the estrogenic component of the AFB1 MOA. Molecular Docking and molecular dynamics simulations were performed to examine the binding affinity of AFB1 and its metabolite aflatoxin Q1 (AFQ1) with the Estrogen Receptors (ERs). Differential gene expression (DGE), gene ontology (GO) and pathway analyses were carried out on hepatic transcriptomic data following in vivo AFB1 exposures. In parallel exposures to the synthetic estrogen ethinylestradiol (EE2) were examined for overlapping effects. Finally, protein-protein interaction (PPI) network analysis assessed the involvement of estrogen responsive targets (ERTs) associated with aflatoxin exposure. The free energies of binding affinity and estimated equilibrium dissociation constants (KD) demonstrated that AFB1 and AFQ1 both interact with ERα and ERβ. DGE and GO analyses highlighted overlap in the responses between AFB1 and EE2 treatments. PPI network analyses following AFBI exposure revealed a dynamic response to AFB1 treatments with solid involvement of ERTs in regulatory networks. This study revealed molecular interactions between aflatoxins (AFB1, AFQ1) and ERs in addition to overlap in DGE and biological processes following AFB1 and EE2 exposures. The estrogenic components at the core of the PPI networks suggest that ER-mediated signaling pathways are a major component in the MOA of aflatoxins.