The goal of the research was to investigate the photocytotoxicity effect and target delivery of polyelectrolyte microcapsules loaded with the photosensitizer chlorin E6 (ClE6) and iron oxide nanoparticles on mouse hepatoma cells (Mh22a). Microcapsules were made by layer by layer (caps-ClE6). Polyelectrolyte layers (PAH and PSS) and iron oxide nanoparticles were alternately deposited on the spherical cores loaded with ClE6. After 24 h incubation of Mh22a with caps-ClE6 (20 caps/cell) and free ClE6 (11.2 μg/mL), the cells were irradiated by red light (660 nm and 60W) for 15 min (RL). The photocytotoxicity was evaluated using MTT colometric tests. The targeting in vitro was determined in a Petri dish after 24 h incubation of cells with caps-CLE6 on a permanent magnet and RL 15 min. The cell death was assessed using double staining (acridine orange and ethidium bromide). For caps-CLE6, the cell viability without RL was more than 70%. In the case of free ClE6, the viability was only 26%. After RL, cell death was 92% and 95% for caps-ClE6 and ClE6,respectively. ROS generation by caps-ClE6 was 2-fold higher compared to free ClE6. After incubation of Mh22a with caps-CLE6 on a permanent magnet and RL, fluorescence microscopy showed almost complete cell death by necrosis and apoptosis and no cell death outside the magnet. Thus, Caps-CLE6 had less dark cytotoxicity with the phototoxicity effect via RL, and could be concentrated with magnets.