The purpose of this investigation was to evaluate a rapid quantitative real-time polymerase chain reaction (PCR) for the direct detection and quantification of pneumococcal DNA bacterial load (DBL) in patients with pneumonia and empyema. DBL and molecular serotype detection was determined by DNA quantification of the pneumolysin (ply) gene and an additional capsular gene by real-time PCR. Plasma or pleural fluid samples from children and adolescents with confirmed pneumococcal pneumonia were analyzed. DBL was correlated with clinical parameters and outcomes. One hundred and sixty-nine patients with pneumococcal pneumonia (145 empyema) had bacterial cultures and real-time PCR assays performed. Among them, 41 (24.3%) had positive results for both, 4 (2.4%) had positive culture alone, and 124 (73.3%) had positive real-time PCR alone. The pleural fluid DBL was lower in patients with prior antibiotics (p = 0.01) and higher in patients with positive culture (p < 0.001). The pleural fluid DBL was positively correlated with serum C-reactive protein (p = 0.009), pleural fluid neutrophils (p < 0.001), and pleural fluid glucose (p < 0.001). The plasma and pleural fluid DBL were higher in patients with ≥8 days of hospital stay (p = 0.002), and the pleural fluid DBL was positively correlated with the number of hours of pleural drainage (p < 0.001). Quantification of pneumococcal DBL by real-time PCR may be helpful for the diagnosis and clinical management of pediatric patients with pneumonia and empyema.