Decomposition of water into oxygen and hydrogen using an electric current was first demonstrated in 1802 by Sir Davy Humphrey. The conclusion of his experiment was that a small electric charge still existed on the electrodes even after the source of the electric current has already been disconnected. However, he was unable to adequately explain this phenomenon.

The basic principle of the fuel cell was discovered in 1838 by the Swiss scientist Christian Friedrich Schönbein, who described it in one of his publications a year later. The article discussed the discovery of ozone and the reaction between oxygen and hydrogen that produced an electrical potential at the electrodes. Sir William Grove, who is considered the "father" of fuel cells, built the first working prototype based on this theoretical work. In 1843, he further wrote about this topic in an article focused on storing electrical energy using gases.

The term "fuel cell" was probably first used by Charles Langer and Ludwig Mond in 1889, when they attempted to develop a cell powered by lamp gas. Despite improvements by William Jacques, who used phosphoric acid as an electrolyte, the cost of manufacturing this cell remained too high. After the invention of the dynamo by Werner von Siemens, the fuel cell fell into obscurity and it wasn’t until 1952 that the first usable prototype with a power output of 5 kW was presented by its inventor, Francis Thomas Bacon. This prototype used potassic hydroxide as the electrolyte.

In the 1960s, the hydrogen fuel cell became an important and highly addressed topic due to space research, because it has a more favourable energy-to-weight ratio compared to other energy sources. Fuel cells were installed, for example, on Apollo spacecrafts and they also powered the Space Shuttles, with each orbiter housing three fuel cells, each with a continuous output of 7 kW and a peak output of 12 kW. One of the main advantages was that the waste product of the hydrogen-oxygen cell was pure water, which could be used in the shuttle's water system.

Since the end of Second World War, the German Navy has been prohibited from using nuclear submarines, and as a result, it was looking for an alternative source of electrical energy. One solution was the use of fuel cells, with cells producing 30 kW of power used in older generations of vessels, and cells producing 120 kW of power used in newer ones. From 2005 to 2008, the first hydrogen highway, called HyNor, with a length of 560 km was put into operation in Norway.

In 2008, a network of hydrogen refuelling stations and fuel cell car rentals was put into operation in the cities of Los Angeles, San Francisco and Las Vegas in the United States. These are Honda FCX Clarity vehicles with a 100 kW PEM fuel cell. In June 2009, the TriHyBus was put into operation in the Czech Republic, which is the first bus with a fuel cell in the former Eastern Bloc. In October 2009, the first hydrogen filling station in the countries of the former Eastern Bloc was commissioned in Neratovice.