A severe form of autoimmune-mediated inflammatory bowel disease (IBD) is termed as ulcerative colitis (UC) which ultimately results in significant mucosal damage and ulceration. Herbal remedies may be employed as an alternative for treatment of UC instead of conventional medications such as Sulfasalazine. Promising natural remedies for the treatment of IBD, including colitis, are propolis extract (PP) and thymoquinone (TQ). This study is aimed at assessing the potential of liposomal formulations of TQ and Egyptian PP in combination therapy on improving their therapeutic efficacy against ulcerative colitis in order to maximize the potential of their beneficial clinical effects. Clinical, biochemical, and histological evaluations of colonic mucosal damage and inflammation were evaluated. The results exhibited a significant increase in tissue MDA, TNFα, and nitrite levels with activation of caspase-3 in the acetic acid-induced colitis group, which is predominantly downregulated in the treatment groups. The prepared formulations of TQ and PP revealed liposomal vesicles in a nanoscale size (192 ± 20.3 and 98.2 ± 20.3 nm, respectively) and accepted stability indicated with a zeta potential of 19.3 ± 0.11 and 17.1 ± 0.25 mV, respectively. They showed an entrapment efficiency of 85.3 ± 12.6% and 69.3 ± 11.8%, respectively. At comparable doses, combination therapy with thymoquinone liposomes and propolis liposomes considerably outperformed free TQ and free PP in reducing inflammation of UC as shown in the present study by clinical, biochemical, and histological evaluations.