Elevated levels of histamine cause the secretion of gastric hydrochloric acid (HCl), leading to gastrointestinal (GI) disorders and anxiety. While aberrant levels of histamine mediate neuroinflammation, pathogenic alterations in the hippocampus of the brain have been linked to anxiety. Eventually, antihistamine drugs that are used against GI disorders appear to be anxiolytic agents. Ranitidine is a widely used antihistamine drug to manage GI disorders as it works by blocking the histamine (H)-2 receptors in oxyntic cells thereby, reducing the HCl production in the stomach. Though some reports indicate the neuroprotective effects of ranitidine, its role against GI disorders related to anxiety remains unclear. Therefore, we investigated the effect of ranitidine against anxiety-related behaviors, neuronal density, and signs of microglia activation in the hippocampal CA3 region of cysteamine HCl-induced mouse model of GI disorder. Results obtained from the open field test (OFT), light and dark box test (LDBT), and elevated plus maze (EPM) revealed that ranitidine treatment reduces anxiety-like behaviors in experimental animals. Nissl staining and immunohistochemical assessment of Iba-1 positive microglia in the cryosectioned brains revealed that the ranitidine treatment enhances the density of pyramidal neurons in association with reduced activation of microglia in the CA3 region of the hippocampus of experimental mice.