Pseuderanthemum palatiferum (Nees) Radlk. is one of the most commonly used medicinal plants in Thailand for treatment of many diseases including cancer. In this study, we investigated the effect of the water fraction of Pseuderanthemum palatiferum ethanol extract powder (WEP) on apoptosis induction in Jurkat cells, and Fourier-transform infrared (FTIR) microspectroscopy was applied to determine biomolecular changes in apoptotic cell death. GC-MS analysis revealed that the major constituents in the extract were 4-Vinylphenol (35.71%), 2-Methoxy-4-vinylphenol (12.12%), 4H-pyran-4-one, 2,3-dihydro-3,5-Dihydroxy-6-methyl-(10.93%), 1-Dodecanlol (6.72%), and Dodecyl acrylate (4.34%). Many other compounds were also detected, but their contents were small. WEP showed selective cytotoxicity to Jurkat cells, while minimal toxicity to normal peripheral blood mononuclear cells (PBMCs) was observed. WEP also induced apoptotic cell death in Jurkat cells as evidenced by the morphological changes, DNA ladder formation, and the release of cytochrome C. FTIR analysis revealed changes of macromolecules with increased intensity of lipid region and decreased intensity of nucleic acid region. Thus, the results confirmed apoptotic induction of WEP against Jurkat cells. This study suggests that a combination of classical biological method and FTIR microspectroscopy could successfully detect biochemical and biophysical features of apoptosis in Jurkat cells.