Background: Colorectal cancer (CRC) is the third most common cause of cancerrelated deaths worldwide. To develop more effective anti-CRC drugs, this research evaluated the impact of synthesized liposomal daunorubicin on HTC116 colon cancer cell line. Methods: Liposomal daunorubicin (LDNR) was synthesized by the thin layer hydration method and size was determined by dynamic light diffraction (DLS). MTT assay was used to determine the cytotoxicity and IC50 of LDNR against the HCT116 CRC cell line. Relative mRNA expression of the NF-κB gene and apoptosis were evaluated in 24 hours treatments of HCT116 cells by qRT-PCR and flow cytometry, respectively. Results: The hydrodynamic diameter of liposomes containing daunorubicin (DNR) was determined 25.2 nm. MTT assay showed a 38% decrease in HCT116 cells viability after 24-hour treatment with the DNR (0.5 μM). The lowest (0.125 μM) and highest (2 μM) dose of LDNR showed 20.4% and 71.6% cytotoxicity, respectively. LDNR showed dose-dependent cytotoxicity with the IC50 of 0.87 μM. The phase contrast microscope evaluation confirmed the LDNR cytotoxicity. The DNR and LDNR (0.87 μM) decreased relative mRNA levels of NF-κB 63% (P= 0.023) and 99.6% (P=0.003), respectively. The percentage of apoptotic cells in the DNR and LDNR increased by 27.1% (P<0.0001) and 49.7% (P<0.0001), respectively. Conclusion: DNR increases the rate of apoptosis by decreasing the NF-κB gene expression in HCT116 cells. These effects are intensified in the liposomal form. Therefore, the LDNR produced in this research can be considered in the treatment of CRC.