In chemistry, "activation" refers to the reversible transition of a molecule into a nearly identical chemical or physical state, with the defining characteristic being that this resultant state exhibits an increased propensity to undergo a specified chemical reaction.  Thus, activation is conceptually the opposite of protection, in which the resulting state exhibits a decreased propensity to undergo a certain reaction.
The energy of activation specifies the amount of free energy the reactants must possess (in addition to their rest energy) in order to initiate their conversion into corresponding products—that is, in order to reach the transition state for the reaction.  The energy needed for activation can be quite small, and often it is provided by the natural random thermal fluctuations of the molecules themselves (i.e. without any external sources of energy).
The branch of chemistry that deals with this topic is called chemical kinetics.