Pelvic lymph node dissection (PLND) is the most accurate procedure for lymph node (LN) staging in prostate cancer (PCa) patients. LN sectioning and hematoxylin and eosin (H&E) staining of at least one slice remains the gold standard for LN evaluation, potentially leading to misdetection of small metastatic focus. Entire LN analysis is possible with One-Step Nucleic Acid Amplification (OSNA) by detecting cytokeratin 19 (CK19) mRNA as a surrogate for LN invasion. This study aimed to compare postoperative performance of OSNA pooling with conventional H&E staining for pathological LN detection in PCa patients. POPCORN was an observational, prospective, and multicenter study of patients with PCa who underwent PLND. Dissected LNs were analyzed by both methods. This study included 2503 LNs from 131 patients, showing no statistically significant differences in pathological LN detection. Concordance between methods was high (93.9%), as were specificity (96.6%) and negative predictive value (96.6%) of OSNA pooling. The measure of agreement (Cohen’s Kappa [κ]) was 0.70. Only eight (6.1%) discordances were observed, including four misdetections from each method. Results showed a high concordance between OSNA pooling and H&E staining, suggesting that OSNA pooling may be a good alternative to H&E staining to detect LN metastases in PCa patients.