Objective: To investigate whether female patients with functional dyspepsia (FD) accompanied by abnormal urinalysis can be distinguished from those with genuine urinary tract infections (UTI), and to compare and analyze potential differences in urinalysis parameters between the two groups while developing a predictive model for differentiation. Methods: This study enrolled 120 female FD patients with abnormal urinalysis and 120 female UTI patients. The Mann–Whitney U test and chi-square test were employed to compare urinalysis parameters and the urinary inflammation index (UII) between the two groups. Receiver operating characteristic (ROC) curve analysis was performed to evaluate the diagnostic efficacy of urinalysis parameters in distinguishing FD from UTIs. Furthermore, logistic regression analysis was conducted to construct a nomogram-based predictive model. Results: Higher levels of leukocyte esterase (500 Leu/μL), positive urinary protein, occult blood (3+), higher red blood cell counts (RBCs ≥ 31/μL), and higher white blood cell counts (WBCs ≥ 71/μL) were associated with an odds ratio (OR < 1), suggesting a stronger association with UTI rather than FD (P < 0.05). In contrast, milder or lower-level abnormalities in urinalysis parameters were more indicative of FD. The optimal combined predictive model for UTI included occult blood, protein, and leukocyte esterase, achieving an AUC of 0.833 (95% CI: 0.778–0.888), with sensitivity, specificity, positive predictive value (PPV), negative predictive value (NPV), and accuracy of 71.7%, 90.8%, 88.6%, 76.2%, and 81.3%, respectively. Conclusion: Abnormal urinalysis indicators in female FD patients exhibit distinct characteristics compared to those in UTI. The combination of urinary protein, leukocyte esterase, and occult blood demonstrates superior predictive value for differentiating between these two conditions. These findings provide a valuable foundation for further investigation into the pathogenesis and therapeutic approaches for FD accompanied by abnormal urinalysis indicators.