Disclosed herein are a deskew apparatus and method for Peripheral Component Interconnect (PCI) Express for compensating for a skew. The deskew apparatus includes a lane data input unit, a lane data alignment unit, and a lane data detection unit. The lane data input unit receives 18-bit data from each of lanes of the PCI Express. The lane data alignment unit aligns the 18-bit data using a COM symbol. The lane data detection unit detects a change in a state of alignment of the 18-bit data attributable to deletion or addition of an SKP symbol when the 18-bit data is aligned, and to perform synchronization between the lanes.