In this study, the traffic operational effects of a pacemaker system (PMS) on the traffic operation in the Geumnam Tunnel on the Seoul–Yangyang Expressway was evaluated herein using a before–after analysis based on long-term vehicle detection system (VDS) data. Changes in spatiotemporal traffic flow and traffic capacity, and speed improvement under different levels of service (LOS) were analyzed using data from five VDS detectors installed upstream and downstream of the tunnel. After PMS installation, (i) increased average and 25th-percentile speeds at most detector locations and decreased standard deviation of speed were observed both near the tunnel exit and the downstream sections, (ii) maximum traffic volume was increased from 1661 to 1765 veh/h/lane (~6.3% increase), (iii) LOS-based speed improvement analysis showed that mean speed and 25th-percentile speed increased by ~6.5%, indicating the alleviation of speed reduction among low-speed vehicles due to PMS. These results prove that PMS increases vehicle speed, reduces speed variability, and enhances traffic flow stability and processing capability. These findings provide empirical evidence supporting the operational effectiveness of a PMS as a practical tool for mitigating phantom congestion in highway tunnel sections and reducing the speed differences between vehicles and improve traffic stream stability.