BODIPY (boron dipyrromethene) derivatives and iron complexes are two types of functional compounds that have found wide applications in the fields of biology and medicine. The new class of cyclometalated Fe(II) complex with NCN pincer and meso‐phenyl‐4'‐ethynyl‐2,2':6',2”‐terpyridine BODIPY ligands of formula [Fe(L)(tpy‐BODIPY)], 1, in which HL:5‐methoxy‐1,3‐bis (1‐methyl‐1H‐benzo[d]imidazol‐2‐yl)benzene, tpy‐BODIPY: 8‐(4‐phenyl‐4'‐ethynyl‐2,2':6',2”‐terpyridine) BODIPY, has been synthesized and studied as mitochondria‐targeted photodynamic therapy (PDT). Complex 1 showed photocytotoxicity in HeLa cells at 500 nm with low dark toxicity. The phototoxicity of complex 1 on the nontumorigenic MRC‐5 cell line showed the same trend observed for HeLa cells, that is moderately photocytotoxic against the nontumorigenic MRC‐5 cell line (IC50 = 36.21 μM). Moreover, complex 1 selectively localizes into mitochondria of the HeLa cells. The photophysical properties, cellular uptake, reactive oxygen species (ROS) generation, and cellular apoptosis of complex 1 have also been studied.Overall, the new Fe(II) complex with BODIPY moiety is significantly photocytotoxic in HeLa cells when irradiated with visible light of 500 nm giving as mitochondria targeting. Therefore, we present cyclometalated Fe(II) pincer complex induced mitochondria‐targeted PDT involving the BODIPY moiety that develops persuasively designed photoactivatable Fe(II) complexes.