Objectives: Breast cancer (BCa) remains the world’s second biggest cause of cancer death. This occurs as a result of unregulated cell development and can be metastasized to other parts of the human. Estrogen receptor alpha is the renowned target that has piqued the interest of researchers to target BCa. FlexX molecular docking technique was used to predict the aspects of interaction, affinities energy, and orientation of natural compounds in the protein site. Phytoconstituents have a vital role in anticancer activities due to their important scaffolds, which may offer more effective and reduced costs and side effects than synthetic drugs. The present study aims to identify new anticancer agents from natural and dietary compounds with lesser adverse effects. Methods: To accomplish this, we implemented with the help of molecular docking approaches using FlexX for predicting the features of bioactive phytocompounds from natural products and evaluating targeted binding affinity energy. Results: Our results confirm that among various natural compounds, daidzein has the best docking score in the ten compounds compared with the standard drug cytarabine. Conclusion: Our study suggests that daidzein is a potent ligand for ERα BCa among all and can be further investigated through in vitro and in vivo studies.