Objective: This study aimed to investigate the relationship between zonulin and intestinal fatty acid-binding protein (I-FABP), biomarkers of intestinal permeability, and cognitive functions in patients with bipolar disorder (BD) compared to healthy controls (HCs). Methods: The study included 40 individuals diagnosed with BD and HCs. Cognitive functions were evaluated using the Stroop Test, Trail Making Test, Öktem Verbal Memory Processes Test, Wisconsin Card Sorting Test, and Digit Span Test. Serum zonulin and I-FABP levels were measured. Results: Zonulin and I-FABP levels were significantly higher in the BD group than in HCs (p ＜ 0.001). After correction for multiple comparisons, significant associations remained between zonulin levels and cognitive performance measures, including the Stroop effect (r = 0.46, p ＜ 0.001), delayed recall (r = −0.41, p ＜ 0.001), and recognition performance (r = 0.42, p ＜ 0.001). No significant correlations were found between I-FABP levels and cognitive test results. Conclusion The observed associations between zonulin levels and cognitive performance suggests a potential relationship of intestinal barrier integrity and gut microbiota with cognitive functions in BD. These findings should be interpreted as associative rather than causal, and future longitudinal studies are required to explore the direction of these relationships.