A substrate processing apparatus includes: a plurality of unit blocks, each having a plurality of modules for processing substrates and a substrate transfer path; a plurality of main transfer mechanisms, each being provided on the substrate transfer path, and configured to transfer the substrates among the plurality of modules; a loading and unloading transfer mechanism configured to load and unload the substrates with respect to each of the unit blocks; a memory configured to store substrate transfer history for each of the unit blocks; and a setting part configured to update a cycle time, which is a time required for a corresponding one of the main transfer mechanisms to move around the substrate transfer path once, of each of the unit blocks based on the substrate transfer history, and configured to set a transfer schedule of the substrates in each of the unit blocks based on the updated cycle time.