An apparatus for preventing a pedestrian collision accident, a system having the same, and a method thereof are provided. The apparatus includes a pedestrian sensing unit that senses a pedestrian moving into a dangerous area and calculates velocity and direction information of the pedestrian. A communication unit transmits the velocity and direction information of the pedestrian to a surrounding vehicle. A time-to-collision (TTC) calculating unit calculates a TTC using velocity and direction information of a subject vehicle and second velocity and direction information of the pedestrian, when the TTC calculating unit receives the second velocity and direction information of the pedestrian from another vehicle. A controller outputs based on the TTC a warning to a driver of the subject vehicle or the pedestrian.