With the spread of information technology in the transportation field, many cities around the globe have introduced smart card systems to stimulate the use of transit services. The systems have resulted in not only the improvement of users’ convenience but also the dramatic changes of travel behaviors with transit services. One prevailing phenomenon is the user’s perception for all transit modes as one single mode in the integrated transit network because of seamless services provided by smart card systems. Although this change has brought tremendous advantages to the dynamics of transit services, it has become more complicated to understand travel behaviors in the integrated transit network which includes features of transfers, service schedule, waiting time and fares. Given that smart card systems have affluent information which can reflect such characteristics, their proper utilizations are still in question. In this sense, when compared with a single-mode network, specific approaches need to be considered to build an integrated transit network from smart card systems, and to develop a suitable model that can reflect the features of the integrated transit network. With smart card systems in the greater Seoul area, Korea, this research proposes methodological techniques which can create the integrated transit network and facilitate transfers automatically between modes. In addition, an attempt is made to verity the applicability of a link-based optimal pathfinding algorithm that has been spotlighted to consider complex travel behaviors in a transit network but has not been proven in the integrated transit network from smart card systems. The concepts of mode-based link labeling and “big node” for transfers are employed with this algorithm. From their applications, optimal transit paths are successfully searched by proposed concepts with smart card data. Given that building an integrated transit network and finding optimal paths are essential tasks for transit analysis studies, this research provides irreplaceable contributions to utilize link-based optimal pathfinding algorithms in the integrated transit network with smart card systems.