Background: Enlarged lymph nodes in adult patients often present a diagnostic challenge. In the absence of granuloma or necrosis, the cytology/tissue findings are misleading and relate the enlarged lymph nodes to reactive lymphoid hyperplasia (RLH), because granuloma formation is an immunological response that usually takes 14–100 days to develop. This study assesses the role of real-time (RT)-PCR in the diagnosis of the Mycobacterium complex (MTBC) in lymph node aspirates compared with culture in cases of RLH. Methods: A cross-sectional study was conducted on 112 patients, aged 15–74 years, with a diagnosis of RLH on cytology. RT-PCR for MTBC detection and culture on Löwenstein-Jensen medium for tubercular bacilli was done on lymph node aspirates. Comparative values with reference to culture were calculated. The χ2 value, positive predictive value (PPV), negative predictive value (NPV), and likelihood ratios (LR) were calculated. Results: Out of 112 RLH cases, 35 (31%) were positive on both RT-PCR and culture. RT-PCR was positive in 43 cases and culture was positive in 44 cases. The χ2 test was found to be highly significant. PPV, NPV, positive LR, and negative LR were 81.4%, 87%, 6.76, and 0.23, respectively. Conclusion: RT-PCR for MTBC proves to be useful in arriving at a conclusive diagnosis in patients with a cytological diagnosis of RLH.