The capacity to identify the unique functional architecture of an individual’s brain is a critical step towards personalized medicine and understanding the neural basis of variations in human cognition and behavior. Here, we developed a novel cortical parcellation approach to accurately map functional organization at the individual level using resting-state fMRI. A population-based functional atlas and a map of inter-individual variability were employed to guide the iterative search for functional networks in individual subjects. Functional networks mapped by this approach were highly reproducible within subjects and effectively captured the variability across subjects, including individual differences in brain lateralization. The algorithm performed well across different subject populations and data types including task fMRI data. The approach was then validated by invasive cortical stimulation mapping in surgical patients, suggesting great potential for use in clinical applications.