Two triazine-cored BODIPY trimers (Compounds 6 and 12) were synthesized and well characterized using 1H NMR, 13C NMR, 11B NMR, 19F NMR, FT-IR, and high-resolution mass spectral analysis. The photophysical, computational, and in vitro anticancer studies of the synthesized compounds were comprehensively evaluated along with previously reported phenylene-BODIPY trimer (Compound 1). The photophysical studies indicated that the triazine-cored BODIPY trimers exhibited a slight bathochromic shift compared to the phenylene-cored trimer. Density functional theory (DFT) calculations suggest that the order of stability of the BODIPY trimers was 1 > 6 > 12. The anticancer efficacy of the BODIPY trimers was investigated against human breast adenocarcinomas cell line MDA-MB-231 and mouse embryo fibroblast cell line NIH/3T3 through in vitro cytotoxicity assay. All the BODIPY trimers exhibited elevated cytotoxicity towards cancer cells while displaying lesser cytotoxicity towards normal cells. Compound 6 showed the highest cell death potential with an IC50 value of 27.02 μM, which is twice higher than that of the chemotherapeutic drug cisplatin. The triazine-cored BODIPY trimers demonstrated superior cytotoxicity against cancer cells in comparison to their phenylene-cored counterparts. The enhanced cytotoxicity of the triazine-cored trimers suggests that the triazine core plays a crucial role in enhancing their therapeutic efficacy. This result underscores the potential of triazine-cored BODIPY trimers as promising anticancer agents.