Functional near-infrared spectroscopy (NIRS) and functional magnetic resonance imaging (fMRI) are non-invasive methods for acquiring hemodynamic signals from the brain with the primary benefit of anatomical specificity of signals. Recently, there has been a surge of studies with NIRS and fMRI for the implementation of a brain-computer interface (BCI), for the acquisition, decoding and regulation of hemodynamic signals in the brain, and to investigate their behavioural consequences. Both NIRS and fMRI rely on the measurement of the task-induced blood oxygen level-dependent response. In this review, we consider fundamental principles, recent developments, applications and future directions and challenges of NIRS-based and fMRI-based BCIs.