The effect of welding heat input on the fatigue life of a quenched boron steel and ferrite-bainite (FB) steel lap joint was investigated. Boron steel was quenched and welded with FB steel in heat input ranging from 0.29 to 0.67 kJ/mm. Boron, which can increase hardenability, affected the microstructure and hardness of the weld metal and heat affected zone (HAZ). The hardness of the weld metal and HAZ increased with decreasing welding heat input, and the high hardness of the weld metal and boron steel HAZ prevented the initiation of cracks in the stress concentration area around the bead. The bead width increased with increasing heat input, and the results of finite element method (FEM) showed that the maximum stress in the notch of the weld joint decreased when the bead width was increased. That is to say, the fatigue life increased when the weld joint had wider bead width. Finally, while the fatigue life was affected by the residual stress, the variation of the welding heat input used in this study had hardly any affect on the residual stress distribution.