The prevalence of constipation, one of the common gastrointestinal (GI) diseases, has been gradually increasing. Gochujang, a traditional Korean fermented paste, has various microbiota and exerts diverse health beneficial effects. However, the ameliorative effect of Gochujang on constipation is unexplored. Seven-week-old ICR mice were divided into five groups: the normal group, the loperamide (LOP) group, the LOP + mosapride citrate (3 mg per kg BW, MOSA) treated group, the LOP + BMG Gochujang (2 g per kg BW) group, and the LOP + VMG Gochujang (2 g per kg BW) group. Gochujang alleviated constipation by increasing defecation frequency and water content in feces by reducing AQP3 mRNA expression. Additionally, Gochujang increased GI transit time and excitatory neurotransmitter levels and decreased inhibitory neurotransmitter levels. Moreover, Gochujang reduced mitogen-activated protein kinase (MAPK) activation and increased the c-Kit/SCF signaling pathway, suggesting that Gochujang regulates the enteric nervous system (ENS). Interestingly, BMG and VMG differently influenced the gut microbiota composition. Both Gochujang groups significantly decreased the Bacteroidetes and Firmicutes ratio compared to the LOP group. However, among Firmicutes genera, Acetatifactor was only reduced in BMG, and VMG only decreased Caproiciproducens and Acutalibacter. In summary, Gochujang effectively alleviated LOP-induced constipation outcomes regardless of their different microbial communities by ameliorating GI motility and changing the gut microbiota composition.