Background: Crataeva nurvala is an important plant having wide application in Ayurveda and Siddha. It is extensively used in formulations for patients suffering from benign prostatic hyperplasia. Objective: Isolation, characterization, and evaluation of cytotoxic activity of bioactive fraction of C. nurvala and identification of molecular target prediction by suitable method. Materials and Methods: Gravity column chromatography followed by HPLC of the bioactive n-butanol fraction afforded compound 1. Besides cell proliferation, apoptotic index and cell migration were studied to determine the efficacy of the compound against cancer cells. Results: The cell cycle analysis revealed that the compound 1 showing apoptosis inducing property through G2/M arrest and mitotic inhibition. Besides, clonogenic assay and wound healing assay demonstrated that the compound could decrease the ability of colony formation and cell migration in a significant way. However, limited availability of the compound impelled us to undertake in silico studies to predictprobable protein targets. This resulted in the identification of IGF1R with highest docking score of −10.0 in preference to four other protein targets (EGFR, AKT1, AKT2, and BCL2) of receptor tyrosine kinase domain (RTKs). As insulin receptor R (Insulin receptor) of tyrosine kinase domain maintains high resemblance with IGF1R, molecular docking was also conducted on the same target. The insignificant docking score suggested specificity of the compound toward IGF1R. Conclusion: The study concluded that; (+)-lyoniresino1-2a-0-β-D-glucopyranoside is a promising apoptosis inducing agent. Molecular modeling of the compound against five crucial protein targets of RTKs suggested that IGF1R could be the probable protein target for the compound.