Friction modifiers (FMs) are widely used in wheel-rail applications. This paper presents a method to analyze the starved elastohydrodynamic lubrication (EHL) of the wheel-rail surface coated with FMs. Combined with rough surface simulation techniques, starved EHL analysis and film thickness analysis, the pressure distribution and adhesion coefficient under different film thickness states are obtained. The effect of film thickness of the FM supply layers and surface roughness on the adhesion coefficient is studied. The adhesion coefficient increases with the decrease in the effective FM film thickness and increase in the surface roughness. Based on the subsurface stress model, the subsurface stress distribution is studied. Then the influence of FMs on the fatigue of wheel and rail is analyzed on the basis of the shakedown map. Finally, the fatigue index of rail is explored in starved EHL state.