During the design phase of a product, reliability and design engineers are called upon to evaluate the reliability of the system, The question of how to meet target reliability for the system arises when estimated reliability or cost is inadequate. This then becomes a problem of reliability allocation and system structure design. This study proposes the optimization methodology to achieve target reliability with minimum cost through construction of the cost function of system. In cost function, total cost means the sum of initial cost, repair cost and maintenance cost. This study constructs optimization problem about system structure design and reliability allocation using cost function. This problem constructed is solved by Multi-island Genetic Algorithm(MIGA), and applies to urban transit brake system. Current brake system of the urban transit is series system. Series system is the simplest and perhaps one of the most common system, but it demands high reliability and maintenance cost because all components must be operating to ensure system operation. Thus this study makes a comparative study by applying k-out-of-n system to brake system. This methodology presented can be a great tool for aiding reliability and design engineers in their decision-makings.