We report on a peculiar X-ray binary pulsar IKT1 = RXJ0047.3-7312 observed with XMM-Newton in Oct. 2000. The X-ray spectrum is described by a two-component spectrum. The hard component has a broken power-law with respective photon indices of 0.2 and 1.8, below and above the break energy at 5.8 keV. The soft component can be modeled by a blackbody of kT = 0.6 keV. The X-ray flux shows a gradual decrease and periodic variations of about 4000 s. The averaged flux in 0.7-10.0 keV is 2.9x10^-12 ergs/cm^2/s, which is ~10 times brighter than that in a ROSAT observation in Nov. 1999. In addition to the 4000-s variation, we found coherent pulsations of 263 +/- 1 s. These discoveries strengthen the Be/X-ray binary scenario proposed by the ROSAT and ASCA observations on this source, and confirm that most of the hard sources in the Small Magellanic Cloud are X-ray binary pulsars. A peculiar property of this XBP is that the coherent pulsations are found only in the soft component, and the folded light curve shows a flat top shape with a sharp dip. We discuss the nature of this XBP focusing on the peculiar soft component.