The rising prevalence of non-alcoholic fatty liver disease NAFLD has strained the healthcare system. Natural products could solve this problem, so the current study focused on the impact of G. thunbergia Thunb. against this ailment. LC–ESI–MS/MS revealed the phytochemical profile of the methanol extract from Gardenia thunbergia leaves (GME). Forty-eight compounds were tentatively identified, and stigmasterol, fucosterol, ursolic acid, and rutin were isolated. The separation of the last three compounds from this plant had not before been achieved. The anti-NAFLD effect of the methanol extract of the leaves of G. thunbergia, and its major metabolite, rutin, was assessed in mice against high-fructose diet (HFD)-induced obesity. Male mice were allocated into nine groups: (1) saline (control), (2) 30% fructose (diseased group), (3) HFD, and 10 mg/kg of simvastatin. Groups 4–6 were administered HFD and rutin 50, 75, and 100 mg/kg. Groups (7–9) were administered HFD and methanol extract of leaves 100, 200, and 300 mg/kg. Methanol extract of G. thunbergia leaves at 200 mg/kg, and rutin at 75 mg/kg significantly reduced HFD-induced increments in mice weight and hepatic damage indicators (AST and ALT), steatosis, and hypertrophy. The levels of total cholesterol, LDL–C, and triglycerides in the blood decreased. In addition, the expressions of CYP2E1, JNK1, and iNOS in the diseased mice were downregulated. This study found that GME and rutin could ameliorate NAFLD in HFD-fed mice, with results comparable to simvastatin, validating G. thunbergia’s hepatoprotective effects.