Silybum marianum seeds contain a family of flavonolignans which can regulate cancer cell proliferation and apoptosis. However, research has rarely focused on the effect of S. marianum essential oil in combination with another anticancer drug. Here, we evaluated the antitumor effect of a combination of 5-fluorouracil (5-FU) and S. marianum essential oils on some pathways in hepatocellular carcinoma (HCC) in vitro and in vivo. Gas chromatography-mass spectrography results indicated there was no significant difference between the components of essential oils isolated from two geographical areas (Khuzestan or Isfahan, Sm-K or Sm-I). Each preparation decreased the viability of H22 cells compared to the control group. S. marianum essential oils alone, and combined with 5-FU, reduced the migration and invasion of H22 cells. Angiogenesis-related proteins were significantly reduced both in vivo and in vitro. Apoptosis and autophagy-related proteins were modulated both in vivo and in vitro. Each treatment decreased phospho-NF-κB (p65) and NF-κB (p65) protein levels. Expression levels of Wnt pathway-related genes were also decreased both in vivo and in vitro. Results revealed that the combination of S. marianum and 5-FU prolonged survival in a mouse model of HCC compared to either treatment alone.