Background: Photodynamic therapy (PDT), a non-invasive treatment modality, has emerged as an effective treatment measure for various cancers, including oesophageal cancer. PDT has attracted much attention in the field of oncology due to its low toxicity profile and the selective accumulation of the photoactivated agent in the tumour cells. However, the therapeutic effect of Aluminium (III) Phthalocyanine Chloride Tetra sulfonic Acid (AlPcS₄Cl) mediated PDT on oesophageal CSCs is limited. In this study, we evaluated the cellular localization of AlPcS₄Cl and its PDT anticancer effects on oesophageal CSCs. Methods: An in vitro experimental design was employed in this study. Oesophageal cancer (HKESC-1 cells) was grown, and the CSCs were isolated using the magnetic-activated cell sorting (MACS). The isolated CSCs were characterised using a flow cytometry, Hoechst efflux side population test, and immunofluorescence. The CSCs were maintained in a serum-free culture medium and incubated at 37° C, 5% CO₂ and 85% humidity. The cells were grouped into control and experimental groups. The CSCs received two-fold increasing concentrations of AlPcS₄Cl and were exposed to irradiation at 673.2nm wavelength using a diode laser. After 24 hours post-PDT, the anticancer activities of AlPcS₄Cl on oesophageal CSCs were examined. The MTT cell viability assay was used to determine the 50% inhibitory concentration (IC50), light microscopy for morphological changes, and adenosine triphosphate (ATP) assay for cell proliferation, lactate dehydrogenase (LDH) assay for cellular toxicity. While cellular localization of AlPcS₄Cl was examined using fluorescent microscopy. All experimental and control cells were conducted in six biological replicates (n = 6). Results: Results were compiled, and statistical analysis was performed using GraphPad Prism (v5). The mean values of experimental groups were compared with the mean value of the control cells. One-way ANOVA was employed, and a p-value of less than 0.05 was considered statistically significant. Findings from cellular localization showed that the AlPcS₄Cl is localized in the mitochondria and lysosomes, indicating a probable cellular death pathway. The dose-response of AlPcS₄Cl on oesophageal CSCs showed an IC50 value of 4µM, suggesting the photosensitizer is efficient for the treatment of CSCs at low concentrations. The CSCs exposed to PDT showed remarkable morphological distortion, high cytotoxic activity, decreased viable cells and significant antiproliferative potential. Conclusions: This study showed that AlPcS₄Cl promote PDT anticancer effects on oesophageal CSCs and could serve as an efficient therapeutic option for eradicating oesophageal CSCs.