Yes. A building permit to replace windows is required for every building in San Francisco, even non-historic buildings. Building permits are required for windows located on the front, rear, and sides of the building. Additional review by the Planning Department is required for all replacement windows that are visible from the street or other public right-of-way. The 2003 revised Residential Design Guidelines require that some property owners use historically appropriate window replacements, such as wood-sash, rather than vinyl or aluminum. Reach out to the Planning Department to ask for the guide to help you choose the appropriate window treatments and to efficiently apply for a permit.
A reminder: Do not purchase replacement windows before confirming with the Planning Department that the windows can be approved. The Planning Department will not approve inappropriate replacement windows, even if they have already been purchased or installed. The Planning Department also strongly suggests repairing, rather than replacing windows.