The basal forebrain cholinergic innervation of the medial prefrontal cortex (mPFC) is crucial for cognitive performance. However, little is known about the organization of connectivity between the basal forebrain and the mPFC in the mouse. Using focal virus injections inducing Cre-dependent enhanced yellow fluorescent protein expression in ChAT-IRES-Cre mice, we tested the hypothesis that there is a topographic mapping between the basal forebrain cholinergic neurons and their axonal projections to the mPFC. We found that ascending cholinergic fibers to the mPFC follow four pathways and that cholinergic neurons take these routes depending on their location in the basal forebrain. In addition, a general mapping pattern was observed in which the position of cholinergic neurons measured along a rostral to caudal extent in the basal forebrain correlated with a ventral to dorsal and a rostral to caudal shift of cholinergic fiber distribution in mPFC. Finally, we found that neurons in the rostral and caudal parts of the basal forebrain differentially innervate the superficial and deep layers of the ventral regions of the mPFC. Thus, a frontocaudal organization of the cholinergic system exists in which distinct mPFC areas and cortical layers are targeted depending on the location of the cholinergic neuron in the basal forebrain.