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The association between <i>H. pylori</i> and small intestinal permeability (IP) on serum testosterone levels in men as mediated by metabolic endotoxemia remains unclear. We sought to explore relationships using correlational analysis between <i>H. pylori</i> IgG class antibody levels and small IP via dual sugar probe analysis on T levels in 50 male participants of reproductive age. Sleep quality, physical activity levels, and Irritable Bowel Syndrome (IBS) symptom severity were measured as potential confounders. Measures for <i>H. pylori</i> (antibodies) increased small IP (lactulose/rhamnose ratio), and hypogonadism (testosterone) did not exceed diagnostic cut-off values for respective pathologies. There was no correlation between lactulose/rhamnose e ratio and GI function markers, zonulin, <i>H. pylori</i>, and IBS questionnaire scores; inflammatory markers, high-sensitivity C-reactive Protein (hsCRP) and Lipopolysaccharide-Binding Protein (LBP); nor endocrine markers, testosterone, Luteinizing hormone (LH), and Follicle-stimulating hormone (FSH). There was a moderate inverse relationship revealed between IBS symptom severity and LBP (r = −0.457, <i>p</i> = 0.004); and hsCRP and testosterone (r = −0.398, <i>p</i> = 0.004). This was independent of physical activity level and sleep quality, but not BMI, which supports the existing link between adiposity, inflammation, and hypogonadism currently present in the literature.