Methods and apparatus for removing sulfur compounds from a hydrocarbon stream are disclosed. In one exemplary embodiment, a method for removing sulfur compounds from a hydrocarbon stream includes the steps of steam stripping a mixed hydrocarbon stream to form a steam stripped overhead stream comprising naphtha and lighter hydrocarbons and a steam stripped bottoms stream comprising naphtha and heavier hydrocarbons; fractionating the steam stripped bottoms stream to form a fractionated overhead stream comprising naphtha hydrocarbons; combining the steam stripped overhead stream with a portion of the fractionated overhead stream and an H2-rich makeup gas stream; and hydrodesulfurizing the combined stream to form an HDS reaction effluent stream.