We introduce here the concept of a transcranial brain atlas (TBA), a new kind of brain atlas specialized for transcranial techniques. A TBA is a probabilistic mapping from scalp space to atlas label space, relating scalp locations to anatomical, functional, network, genetic, or other labels. TBAs offer a new way to integrate and present structural and functional organization of the brain and allow previously subsurface and invisible atlas labels visible on the scalp surface to accurately guide the placement of transcranial devices directly on the scalp surface in a straightforward, visual manner. We present here a framework for building TBAs that includes (i) a new, continuous proportional coordinate system devised for the scalp surface to allow standardized specification of scalp positions; (ii) a high-resolution, large sample-based (114-participant) mapping from scalp space to brain space to accurately and reliably describe human cranio-cortical correspondence; and (iii) a two-step Markov chain to combine the probabilistic scalp-brain mapping with a traditional brain atlas, bringing atlas labels to the scalp surface. We assessed the reproducibility (consistency of TBAs generated from different groups) and predictiveness (prediction accuracy of labels for individuals without brain images) of the TBAs built via our framework. Moreover, we present an application of TBAs to a functional near-infrared spectroscopy finger-tapping experiment, illustrating the utility and benefits of TBAs in transcranial studies. Our results demonstrate that TBAs can support ongoing efforts to map the human brain using transcranial techniques, just as traditional brain atlases have supported magnetic resonance imaging and positron emission tomography studies.