Abstract Lactoferrin is a multifunctional protein mainly involved in the immune defense of organisms against various pathogens. It has been reported that intestinal inflammation was reduced by lactoferrin administration. However, the precise mechanism underlying lactoferrin’s involvement in intestinal inflammation is not yet fully understood. In this study, we purified a mouse intestinal lactoferrin-binding protein with a molecular mass of ~ 400 kDa that was expressed in the small intestine and colon. Sequence analysis revealed that the intestinal lactoferrin-binding protein represented an ortholog of rat immunoglobulin G fragment crystallizable gamma-binding protein (IgGFcγBP). N-linked glycans of lactoferrin were not necessary for binding to IgGFcγBP. After reduction, IgGFcγBP was separated into 120, 70, 65, 60, and 55 kDa proteins, but these did not bind to lactoferrin. The expression of IgGFcγBP was lost in a mouse model of dextran sodium sulfate induced colitis and restored during the convalescence period of colitis, suggesting a role in mucosal protection and immune regulation. Furthermore, we discuss potential links between IgGFcγBP and mucin-associated microbiota which may contribute to lactoferrin’s immunomodulatory effects. These findings provide new insights into the interaction between lactoferrin, mucosal immunity, and gut microbiota.