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Introduction: Chronic kidney disease (CKD) which is a common cause of death has an increasing trend, but there is no established approach for predicting CKD progression yet. Functional magnetic resonance imaging (fMRI) studies such as blood oxygenation level‐dependent MRI (BOLD‐MRI), diffusion‐weighted MRI (DWI‐MRI), diffusion‐tensor MRI (DTI‐MRI) and arterial spin labelling MRI (ASL‐MRI) are rising methods for the assessment of kidney functions in native and transplanted kidneys as well as the estimation of CKD progression. Methods: Systematic literature review was performed through the Embase (Elsevier), Cochrane Central Register of Controlled Trials (Wiley), PubMed/Medline and Web of Science databases, and studies investigating the role of fMRI methods assessing kidney functions in native and transplanted kidneys, as well as the value of fMRI methods to predict CKD progression, were included. Working mechanisms, advantages and limitations of the fMRI modalities were reviewed, and three studies investigating the role of fMRI studies in kidney functions were analysed. Results and conclusion: BOLD‐MRI signal was found to be inversely correlated with annual eGFR change, and DWI/ADC (apparent diffusion coefficient map) values were shown to be correlated with annual eGFR decline. fMRI methods which are currently used for other systems can be utilized to provide more detailed information about kidney functions, and doctors should be ready to interpret kidney MRIs. [ABSTRACT FROM AUTHOR]