Background: The correlation between small intestinal bacterial overgrowth (SIBO) and nonalcoholic fatty liver disease (NAFLD) has gained heightened acknowledgment, especially in the late phases of liver disease. Despite this, studies focusing on the prevalence and specific characteristics of SIBO within the steatotic liver disease patient population in Pakistan remain sparse. This research seeks to investigate the prevalence and characteristics of SIBO in patients with fatty liver disease in a tertiary healthcare facility in Karachi. Materials and methods: Conducted from July 2023 to March 2024 at Ziauddin Medical University Hospital’s Clifton Campus, this prospective cross-sectional study included 65 adults aged 18–80 diagnosed with NAFLD via FibroScan®. The evaluation of small bowel microbial overgrowth was established by a glucose hydrogen breath test (GHBT), where a rise in hydrogen concentration of ≥20 ppm from the initial measurement within two hours signifies a good outcome. Participant demographics, comorbid conditions, and clinical symptoms were documented. Results: Of the 65 individuals, 46 were male, with an average age of 44.88 ± 12.30 years, a mean index of body mass of 26.45 ± 6.45 kg/m2, and an average waist measurement of 95.20 ± 15.17 cm. Lean NAFLD was observed in 40% of the participants. Frequent comorbidities included diabetes (40%), hypertension (38%), and dyslipidemia (38%). Small intestinal bacterial overgrowth was identified in 37% of the subjects, 28% of whom were asymptomatic. Symptoms prevalent in SIBO-positive individuals were bloating (41%), belching (26%), and abdominal pain (28%). Liver stiffness indicated that 23% had F2 fibrosis, 28% had F3, and 49% had F4. Controlled attenuation parameter (CAP) scores showed S1 steatosis in 37% of patients, S2 in 29%, and S3 in 34%. The presence of SIBO correlated with increasing fibrosis and steatosis levels. Small intestinal bacterial overgrowth (SIBO) positivity was more prevalent in the high Child-Pugh class and more severe liver dysfunction. With post-treatment giving Lactobacillus reuteri and rifaximin for two weeks, only 4% remained SIBO-positive. Significant associations of SIBO were also noted with dyslipidemia, hyperuricemia, and irritable bowel syndrome. Conclusion: This research highlights a significant incidence of SIBO in NAFLD individuals, particularly those with severe liver damage and comorbidities. It stresses the importance of regular screening for SIBO in such patients, suggesting that timely detection and intervention could enhance patient outcomes.