Alkaline fuel cells utilize an aqueous alkaline electrolyte (most commonly potassium hydroxide) to conduct hydroxide ions from the cathode to the anode. Solid-state alkaline fuel cells using anion exchange membranes have also been experimented with. Water is formed at the anode, and an electron flow is generated in the external circuit.

Alkaline fuel cells are the oldest type of hydrogen fuel cells. They were invented in 1932 and used by NASA for the Apollo missions from 1968 to 1972. While alkaline fuel cells have largely been replaced by PEM or solid oxide alternatives, they are still used in spacecraft applications due to their high energy efficiency and reliability.

Proton Exchange Membrane (PEM) fuel cells, also known as polymer electrolyte membrane fuel cells, operate by supplying hydrogen at the anode, where it is oxidized using a catalyst. Hydrogen ions travel through the PEM to the cathode, while electrons flow to the cathode via an external load circuit. At the cathode, oxygen is reduced and combines with hydrogen ions to form water. The flow of electrons generates an electric current, providing the power output of the PEM fuel cell.

Compared to other hydrogen fuel cells, hydrogen PEM fuel cells operate at lower temperatures (typically 50–100 °C) while delivering high power density and fast startup times. They are primarily used in transportation.

Phosphoric acid fuel cells (PAFCs) use a liquid phosphoric acid electrolyte. Similar to PEM fuel cells, hydrogen ions travel through the electrolyte to the cathode, while electrons flow through the external load circuit. At the cathode, hydrogen ions combine with oxygen to form water.

Compared to other hydrogen fuel cells, PAFCs exhibit greater tolerance to impurities such as CO₂ in the fuel stream. This allows them to use hydrogen produced via steam reforming, which releases CO₂ as a byproduct.PAFCs operate at temperatures between 150–200 °C, enabling efficient waste heat recovery without the extreme temperatures associated with solid oxide fuel cells.

Solid oxide fuel cells (SOFCs) are highly durable and energy-efficient, making them ideal for applications where waste heat can be utilized. Unlike PEM fuel cells, SOFCs have long startup times and operate at very high temperatures, up to 1,000 °C, which makes them unsuitable for most transportation applications. Development of SOFCs has been focused primarily on stationary generators for buildings, such as hospitals and data centers.

Another notable feature of solid oxide fuel cells (SOFCs) is their ability to utilize a variety of fuels, such as hydrogen, carbon monoxide, and natural gas, providing flexibility in fuel sources.