Traffic congestion in tunnels, particularly phantom jams, significantly reduces driving efficiency and increases crash risks. To address this issue, a Pacemaker System (PMS) was implemented in the Geumnam Tunnel along the Seoul–Yangyang Expressway. A PMS aims to stabilize traffic flow and improve operational efficiency by guiding drivers to maintain uniform speeds through sequential LED illumination. This study aims to quantitatively evaluate the effectiveness of a PMS on traffic flow by analyzing Vehicle Detection System (VDS) data collected before and after its implementation. The analysis incorporated Level of Service (LOS) categories A–E, and distinguished between peak and non-peak hours to assess speed improvements and flow stabilization. The results indicated that the PMS increased the average speeds by approximately 6.5% across the LOS A–E conditions, with the most pronounced effects observed in LOS C–E. Furthermore, the speed distribution analysis revealed that the PMS enhanced lower-percentile speeds and reduced speed variance, thereby contributing to improved traffic stability. Statistical tests confirmed that the observed improvements were significant (p < 0.05). These findings demonstrate that the PMS effectively mitigates phantom jams and improves tunnel traffic efficiency, offering empirical evidence to support future PMS deployment and the development of tunnel traffic management policies.