The worldwide increasing demand for environmentally-friendly transportation fuels and the strict regulations by the environmental protection agencies have put a great pressure on crude oil refining and upgrading industry. The main current technology for the desulfurization of crude oil and its fractions is hydrodesulfurization. However, this process is plagued with several drawbacks. The growing pressure on petroleum refining industries to reduce sulfur contents in fuels has made hydrodesulfurization process even more unappealing. Hence, more effective alternatives have been (and are still) sought by petroleum refining industries. Enzymatic desulfurization process has recently emerged as a promising alternative that has the potential to be cost-effective, efficient and environmental-friendly. In enzymatic desulfurization process, enzymes (whether intracellular or extracellular) attack organosulfur components in the crude oil or its fractions and remove sulfur through a series of enzymatic reactions. The process is an energy-saving process, devoid of emission of harmful gases into the atmosphere, and utilizes completely biodegradable catalysts. This article reviews the recent progress in desulfurization of crude oil and its fractions using extracellular and intracellular enzymes. Challenges encountered during enzymatic desulfurization are highlighted, and some potential solutions to tackle the challenges are proposed. Future outlooks into the development of more efficient enzymatic desulfurization processes have been pinpointed.