Methods for removing sulfur from hydrocarbon streams using the sequential application of hydrodesulfurization, fractionation and oxidation. The hydrodesulfurization step is operative to remove easily-hydrogenated sulfur species, such as sulfides, disulfides and mercaptans. The resultant stream is then fractionated at a select temperature range to generate a sub-stream that is sulfur-rich with the sulfur species resistant to removal by hydrodesulfurization. The sub-stream is then isolated and subjected to an oxidative process operative to oxidize the sulfur species to sulfones or sulfoxides, which may then be removed by a variety of conventional methods, such as absorption. Alternatively, the methods may comprise using the sequential application of fractionation to generate a sulfur-rich sub-stream followed by oxidation and subsequent removal of the sulfur species present in the sub-fraction. The latter methods are ideally suited for transmix applications.