Photodynamic therapy (PDT) using photosensitizer (PS)‐embedded silicone membrane‐covered self‐expandable metallic stents (SEMSs) can function in palliative therapeutic option for malignant gastrointestinal tract obstruction. However, stent‐related complications should be considered, and accurate delivery of light sources is technically difficult. Here, a Chlorin e6 (Ce6)‐an embedded stent‐based catheter is developed to improve its therapeutic efficacy and safety. PDT using Ce6‐embedded stent successfully induced cell death of colorectal cancer cell line. PDT‐treated liver tissues showed an increase in ablation depth in proportion to irradiation energy, and 600 J/cm2 demonstrates an even and sufficient ablation depth. Endoluminal PDT using the Ce6‐embedded stent‐based catheter was technically successful in a rat colon model without procedure‐related complications such as colonic perforation or stricture formation. The results in colonoscopy, colonography, and histological examination, along with statistical analysis, suggest that a novel PDT modality using a Ce6‐embedded stent‐based catheter was safely conducted and demonstrated apoptotic cell death at 12 h after PDT, and it gradually recovered from 2 to 4 weeks. Thus, the PDT using the Ce6‐embedded stent‐based catheter may represent a promising new approach for the treatment of malignant colorectal obstruction.