A recent study on folate binding protein (FBP), the soluble form of a folate receptor (FR), revealed surprising inhibition of in vivo growth of KB cell-derived xenograft tumors in mice and the induction of in vitro caspase-mediated apoptosis in KB, HeLa, and A549 cells in culture. In this research, we investigated the mechanism(s) underlying FBP-induced cytotoxicity and apoptosis in FR-overexpressing KB cancer cells using next-generation sequencing (NGS), a high-throughput technology for RNA sequencing and gene expression profiling, followed by bioinformatics analysis. The transcriptomics data, in addition to immunofluorescence analyses, indicated over and under expression of many proteins and transcription factors, such as Snail1, MCP-1 (CCL2), ZFP36, and HOXA9 in KB cells after treatment with 50 μM FBP for 6, 12, and 24 h. The alteration of an expression level in these genes, which are involved in epithelial to mesenchymal transition (EMT), inflammatory, and apoptosis pathways, is consistent with the induction of folate deficiency in FBP-exposed KB cells. The temporal effect of 50 μM FBP on DNA breakage and the induction of apoptosis, examined by the TUNEL assay, also supports the hypothesis of FBP-mediated folate deprivation of KB cells. The evidence reported in this study sheds light on the mechanism of FBP cytotoxicity in FR-overexpressing KB cancer cells in culture and suggests possible pathways for the observation of inhibited growth for KB xenograft tumors in vivo.