Background: Proton pump inhibitors (PPIs) are widely prescribed for gastrointestinal disorders but may influence urinary solute handling and increase the risk of nephrolithiasis. Evidence regarding their effect on kidney stone formation and urinary chemistry remains limited. Objectives: To study the correlation between PPI use and incident nephrolithiasis and to assess its impact on 24-hour urine chemistry. Methods: This comparative research has been performed at the Department of Urology, Faculty of Medicine, Suez Canal University, including 456 adult cases identified with gastroesophageal reflux disease (GERD) and without prior nephrolithiasis. Participants have been separated into two groups: PPI users (number = 228) and non-users (number = 228). The primary outcome was kidney stone formation, assessed by patient history, clinical evaluation, and imaging. Secondary outcomes included stone recurrence and 24-hour urine analysis. Results: Clinical characteristics and baseline demographics have been balanced between groups, except for higher rates of hypertension and hyperlipidemia among PPI users. Stone composition did not differ significantly. However, PPI users had significantly lower urinary calcium, citrate, magnesium, phosphorus, sulfate, and supersaturation of calcium phosphate compared with non-users (all p below 0.05). Multivariable regression confirms independent correlations between PPI use and reductions in these urinary parameters. Insignificant variances have been observed for urinary volume, oxalate, pH, uric acid, or supersaturation of calcium oxalate. Conclusion: PPI use was associated with distinct alterations in urinary chemistry that may predispose to nephrolithiasis. These findings highlight the need for careful monitoring of kidney stone risk in long-term PPI users.