Harrat Lunayyir is one of the youngest Cenozoic volcanic fields in western Saudi Arabia, which in 2009 experienced a seismic swarm of about 34,000 events with a maximum magnitude of M5.4. Many studies debated about the relationship of a depicted shallow-level magma intrusion with the Red Sea rifting and the channelized northward flow from the Afar mantle plume. In this study, a detailed seismic tomography inversion for the P- and S-wave velocities, and the Poisson’s ratio structures beneath Harrat Lunayyir and the adjacent Red Sea offshore area is presented. The tomographic images showed evidence of magma intrusions beneath the Lunayyir Swarm Area (LSA) characterized by low P- and S-wave velocity and high Poisson’s ratio anomalies down to 21 km depth. These anomalies are in juxtaposition with some high-velocity anomalies attributed to remnants of solidified magma intrusions relevant to previous episodes of volcanicity. Beneath the Red Sea, the lithospheric mantle structure is clearly observed as a high P-wave velocity high-Poisson’s ratio anomaly at a depth of 20–40 km. Traces of high-Vp anomalies with anomalous Poisson’s ratio are observed in the area between the Red Sea and the LSA suggesting that a channel of hot lithospheric mantle material may link the Red Sea rift structure with the LSA. We suggest that the Red Sea drifting and its related processes in the Zabargad Shear Zone might have significantly contributed to the early formation of the Lunayyir volcanic field and could possibly have in an impact on any magmatic activity in the future.