Cirrhosis and hepatic encephalopathy (HE) is associated with an altered gut–liver–brain axis. Fecal microbial transplant (FMT) after antibiotics improves outcomes in HE, but the impact on brain function is unclear. The aim of this study is to determine the effect of colonization using human donors in germ‐free (GF) mice on the gut–liver–brain axis. GF and conventional mice were made cirrhotic using carbon tetrachloride and compared with controls in GF and conventional state. Additional GF mice were colonized with stool from controls (Ctrl‐Hum) and patients with cirrhosis (Cirr‐Hum). Stools from patients with HE cirrhosis after antibiotics were pooled (pre‐FMT). Stools from the same patients 15 days after FMT from a healthy donor were also pooled (post‐FMT). Sterile supernatants were created from pre‐FMT and post‐FMT samples. GF mice were colonized using stools/sterile supernatants. For all mice, frontal cortex, liver, and small/large intestines were collected. Cortical inflammation, synaptic plasticity and gamma‐aminobutyric acid (GABA) signaling, and liver inflammation and intestinal 16s ribosomal RNA microbiota sequencing were performed. Conventional cirrhotic mice had higher degrees of neuroinflammation, microglial/glial activation, GABA signaling, and intestinal dysbiosis compared with other groups. Cirr‐Hum mice had greater neuroinflammation, microglial/glial activation, and GABA signaling and lower synaptic plasticity compared with Ctrl‐Hum mice. This was associated with greater dysbiosis but no change in liver histology. Pre‐FMT material colonization was associated with neuroinflammation and microglial activation and dysbiosis, which was reduced significantly with post‐FMT samples. Sterile pre‐FMT and post‐FMT supernatants did not affect brain parameters. Liver inflammation was unaffected. Conclusion: Fecal microbial colonization from patients with cirrhosis results in higher degrees of neuroinflammation and activation of GABAergic and neuronal activation in mice regardless of cirrhosis compared with those from healthy humans. Reduction in neuroinflammation by using samples from post‐FMT patients to colonize GF mice shows a direct effect of fecal microbiota independent of active liver inflammation or injury.