Silymarin and thymoquinone exert neuroprotective effects, although their combined effects in focal cerebral ischemia/reperfusion (I/R) models are unknown. We compared the effect of silymarin and thymoquinone in an I/R rat model. Wistar rats were divided into five groups: SHAM, REP (I/R), SIR (200 mg/kg silymarin+I/R), TIR (3 mg/kg thymoquinone+I/R), and STIR (200 mg/kg silymarin+3-mg thymoquinone+I/R). The rats underwent bilateral carotid artery occlusion for 30 min and neurological assessments 24 h thereafter. Apoptosis was evaluated using anti-caspase-3 and terminal deoxynucleotidyl transferase biotin-dUTP nick end labeling (TUNEL) assays. Astrocyte activation was determined using an anti-GFAP antibody. Total antioxidant status (TAS), total oxidant status (TOS), and trimethylamine N-oxide (TMAO) levels were measured. SHAM and REP rats had the lowest and highest neurological scores, respectively (p = 0.001). REP rats showed greater deterioration than SIR, TIR, and STIR rats. SIR, TIR, and STIR rats had fewer TUNEL and caspase-3-positive cells than REP rats (p<0.05). GFAP expression was higher in REP rats (p<0.05) than in SIR, TIR, and STIR rats (p<0.05). SIR and TIR rats showed higher TAS than REP rats (p<0.05). SIR, TIR, and STIR rats had lower TMAO values than REP and SHAM rats (p<0.05). Silymarin/thymoquinone reduces impairment, apoptosis, and astrocyte activation. Combination therapy reduces TMAO levels.