Disclosed is a clock phase aligning apparatus capable of synchronizing a clock signal in the middle of an upstream burst mode data bit in an optical line terminal of a passive optical network. The clock phase aligning apparatus effectively aligns a phase of a clock signal with a phase of data during an overhead period of burst mode packet data through an over-sampling scheme and a digital scheme. Burst mode data signals are subject to an over-sampling through a high speed continuous mode analog circuit and then converted into low speed parallel signals through a parallel conversion unit. Such low speed parallel signals are processed with respect to sampling patterns through a digital look-up scheme in a logic circuit device such that the phase of data is arranged with the phase of a clock signal during a limited bit stream specified in a burst mode preamble timing.