Modeling hydrocarbon flow, from layered shale formations. At least some of the illustrative embodiments are methods including: modeling movement of hydrocarbons through kerogen-related porosity, the movement through a first model volume; estimating a first permeability of a kerogen-rich layer of a layered shale formation based on the modeling; and modeling hydrocarbon production from the layered shale formation. The modeling hydrocarbon production may include: utilizing the first permeability for the kerogen-rich layer of the layered shale formation; and utilizing a second permeability for a kerogen-poor layer of the layered shale formation, the second permeability different than the first permeability. In various cases the modeling of hydrocarbon production is with respect to a second model volume greater than the first model volume.