Railway overhead traction system is a classic example of scattered conductor configuration, where tracks and other wires form multi-conductor transmission lines (MTLs) with large variation in conductor heights above ground and they are spread across regions having different soil conditions. Lightning transient analysis in such systems has not received much attention earlier. Here we analyze the influence of conductor heights and lossy ground on the induced voltages in a two conductor MTLs for the case of a direct lightning strike. For transient analysis, modified time domain transient ground impedance expressions having better early and late time behavior was used. The dependence of transient ground impedance on conductor heights and ground resistivity are presented and discussed. The early time transient ground impedances are unaffected by ground resistivity but their decaying nature is highly dominated by ground resistivity. It is found, if one of the conductors is close to ground (a rail) and if it is at large vertical distance from struck conductor (an auxiliary power line), then with increasing ground resistivity the peak induced voltages in the conductor close to ground initially increase, then decrease and finally tend to remain constant (within 100–10,000 Ω m). This phenomenon is opposite to that compared to conductors that are close to each other with minimum vertical separation (two auxiliary power lines), where the peak induced voltages increase with increasing ground resistivity. The study focuses mainly to access when a mutual coupling due to system geometry or due to ground losses becomes dominant in determining induced effects from lightning in MTLs, which could be an important contribution to the lightning interaction studies for electrified railway systems.