Functional magnetic resonance imaging has become a primary tool for psychological and cognitive studies or preclinical brain research. As a technique to map brain function, fMRI measures the blood oxygenation level–dependent signal as a collective effect of changes in cerebral blood flow, cerebral blood volume, and cerebral metabolic rate of oxygen following changes in neural activity. The use of fMRI in combination with carefully designed task paradigms has enabled scientists to map perceptual, cognitive, or behavioral functions onto brain regions and networks. Spontaneous activity observed with fMRI in task-free resting states has been used to reveal intrinsic functional networks that collectively depict the brain’s functional architecture or connectome. Naturalistic paradigms for fMRI are increasingly used to map brain activation, address neural representation and coding, and characterize brain networks while humans are engaged in a realistic and dynamic environment similar to daily life experiences. In this chapter, we discuss the principles, methods, and applications of fMRI, with emphasis on its biophysical and physiological basis, experimental designs and analysis methods, and applications to human and animal studies. Example data or results from empirical studies are presented to help illustrate methods or support scientific views.