Insect cell lines have been utilized as an important higher eukaryotic model system to decipher stress responses and cell death mechanisms. Lepidopteran Sf9 cells (derived from the ovaries of Spodoptera frugiperda) display nearly 100 times higher resistance to ionizing radiation in contrast to mammalian cells, which is partly contributed by an unusually high HDAC activity. However, their response to HDAC inhibition remains to be evaluated. In the present study, the effects of HDAC inhibitor (NaBt) on Sf9 cellular/nuclear morphology, cell cycle progression, DNA damage/repair, redox status, and mitochondrial perturbations were evaluated. NaBt-induced apoptosis was evident at 18 h in Sf9 cells at 2 mM concentration, primarily through mitochondrial induction of oxidative stress and subsequent DNA damage. Cell cycle analysis revealed appearance of sub-G1 DNA content at 12 h onwards and DNA fragmentation by 18 h. Initial few hours of treatment caused significant loss in MMP through oxidation of mitochondrial inner membrane protein, i.e., cardiolipin. HDAC inhibition-mediated apoptosis was associated with increased Bax/Bcl2 ratio, mitochondrial cytochrome-c release, and caspase-3 activation. The study thus infers that Sf9 cells, which can withstand very high radiation doses, are quite sensitive to the increase in the chromatin acetylation levels. In addition, HDAC inhibition also sensitized Sf9 cells to radiation-induced DNA damage, further corroborating our recent finding that chromatin compactness contributes significantly to their radioresistance. Therefore, the study demonstrates prominence of prevailing DNA/chromatin protective mechanisms in Lepidopteran insect cells.