A printed substrate design system includes: an EMI condition determination unit that compares an EMI characteristic derived by an EMI characteristic derivation unit with an EMI allowable condition, and determines whether the EMI characteristic of a printed substrate satisfies the EMI allowable condition; a substrate configuration change unit that changes an internal configuration of the printed substrate to obtain a changed configuration of the printed substrate in a case where the EMI condition determination unit has determined that the EMI allowable condition is not satisfied, and sets design information of the changed configuration of the printed substrate to design information for deriving the EMI characteristic in the EMI characteristic derivation unit; and an output unit that outputs a printed substrate configuration in a case where the EMI condition determination unit has determined the EMI allowable condition is satisfied.