Conventional transportation systems are facing many challenges related to reducing fuel consumption, noise, and pollutants to satisfy rising environmental and economic criteria. These requirements have prompted many researchers and manufacturers in the transportation sector to look for cleaner, more efficient, and more sustainable alternatives. Powertrains based on fuel cell systems could partially or completely replace their conventional counterparts used in all modes of transport, starting from small ones, such as scooters, to large mechanisms such as commercial airplanes. Since hydrogen fuel cells (HFCs) emit only water and heat as byproducts and have higher energy conversion efficiency in comparison with other conventional systems, it has become tempting for many scholars to explore their potential for resolving the environmental and economic concerns associated with the transportation sector. This paper thoroughly reviews the principles and applications of fuel cell systems for the main transportation schemes, including scooters, bicycles, motorcycles, cars, buses, trains, and aerial vehicles. The review showed that fuel cells would soon become the powertrain of choice for most modes of transportation. For commercial long-rage airplanes, however, employing fuel cells will be limited due to the replacement of the axillary power unit (APU) in the foreseeable future. Using fuel cells to propel such large airplanes would necessitate redesigning the airplane structure to accommodate the required hydrogen tanks, which could take a bit more time.