Functional neuroimaging studies have revealed the importance of the role of cognitive and psychological factors and the dysregulation of the brain-gut axis in functional gastrointestinal disorder patients. Although only a small number of neuroimaging studies have been conducted in functional gastrointestinal disorder patients, and despite the fact that the neuroimaging technique requires a high level of knowledge, the technique still has a great deal of potential. The application of functional magnetic resonance imaging (fMRI) technique in functional gastrointestinal disorders should provide novel methods of diagnosing and treating patients. In this review, basic knowledge and technical/practical issues of fMRI will be introduced to clinicians.