Background: Short-chain fatty acids (SCFA) are the main metabolites of the intestinal microbiota, which play a role as colonocyte trophic factors and maintain the integrity of the gastrointestinal tract and blood-brain barrier. Microbiota dysbiosis that occurs in cirrhosis reduces SCFA production and plays a role in the pathogenesis of hepatic encephalopathy (HE). This study aims to compare the amount and composition of fecal SCFA in patients with cirrhosis, with and without HE. Methods: This research is a cross-sectional study at the Hepatobiliary Clinic and Integrated Procedure Room, Dr. Cipto Mangunkusumo Hospital, Jakarta, in 2023. Patients with cirrhosis underwent a flicker or Stroop test, fecal SCFA examination (acetate, butyrate, and propionate), and a questionnaire with a food recall technique to assess dietary patterns. Results: A total of 86 patients with cirrhosis participated in this study, with a mean age of 53 ± 8.10 years, and the majority were male (68.6%). Hepatic encephalopathy (HE) was identified in 20 patients (23.25%). Multivariable analysis of SCFA profiles showed no statistically significant associations with HE. The absolute SCFA proportion had an adjusted prevalence ratio (PR) of 1.98 [95% CI: 0.75–5.24; p = 0.171], the absolute acetate proportion had an adjusted PR of 2.06 [95% CI: 0.40–10.62; p = 0.388], and the butyrate proportion had an adjusted PR of 2.02 [95% CI: 0.76–5.39; p = 0.158]. Conclusion: Changes in SCFA composition may be associated with the presence of HE in patients with cirrhosis. Although no statistically significant relationships were found, these findings suggest that SCFA profiles warrant further investigation concerning dysbiosis and HE in cirrhosis. © 2025, Indonesian Society of Internal Medicine. All rights reserved.