Functional magnetic resonance imaging (fMRI) is a widely used technique for studying brain substrates of cognition. The objective of this chapter is to provide an overview of the basics of fMRI including fundamentals of MR physics and the blood oxygen level dependent (BOLD) contrast, paradigm design, data storage, image quality analysis, data pre-processing and data analytic strategies. We have discussed three illustrative examples from our published research works in schizophrenia, a neurodevelopmental disorder characterized by cognitive dysfunction and abnormalities of thought, perception and conation. We attempt to provide a broad understanding of the basic principles of fMRI research for clinicians and budding cognitive neuroscience researchers alike, without aiming to be exhaustive or in-depth in our coverage. We hope this primer in fMRI methods and applications would motivate the reader to peruse the additional resources cited at the end of the chapter while getting started in this exciting area of research.