Ischaemic stroke can induce rapid activation of microglia. As the resident immune cells of the central nervous system, microglial activation is believed to play a central role in neuroinflammation and pathological progression of ischaemic tissue. The activation of microglia after ischaemia involves several stereotypical events including morphological transformation, proliferation and polarisation. Studies using confocal or two-photon imaging techniques have revealed that the degree of microglial activation is correlated with the degree of ischaemia. Activated microglia display diverse polarisation phenotypes. It remains largely unclear regarding whether activated microglia are beneficial or detrimental to poststroke recovery. This mini-review focuses on the morphological and functional aspects of microglial activation, with particular attention to progress in two-photon imaging studies.