Secondary fuels are fuels that are derived from some primary fuel or fuels through chemical or physical processes. These are fuels that are not found as a natural resource. The energy for these secondary fuels comes initially from primary energy sources.
Gasoline is the best example of a secondary fuel, as it must be made from oil through distillation processes. While many of the actual chemicals in gasoline are found in crude oil, they must be separated out in order to put the hydrocarbons in the most useful form.
Molecular hydrogen can be a secondary fuel as well, but this is often made in a fuel cell. This process allows water to be separated into hydrogen and oxygen, but the energy to do this must come from a primary energy source (either another fuel like coal or a flow like hydropower).
Secondary fuels are often made to maximize the ability for combustion to get energy into an engine. This means that secondary fuels are often an intermediate form of energy between the primary energy and the energy services. This intermediate form is also known as an energy currency but energy currencies also include electricity which not a fuel (see electricity as an energy currency).