This paper presents development of an X-ray pixel detector with a multi-port charge-coupled device (MPCCD) for X-ray Free-Electron laser experiments. The fabrication process of the CCD was selected based on the X-ray radiation hardness against the estimated annual dose of 1.6 × 10(14) photon/mm(2). The sensor device was optimized by maximizing the full well capacity as high as 5 Me- within 50 μm square pixels while keeping the single photon detection capability for X-ray photons higher than 6 keV and a readout speed of 60 frames/s. The system development also included a detector system for the MPCCD sensor. This paper summarizes the performance, calibration methods, and operation status.