A method and apparatus for avoiding a collision of an uplink preamble using a cell identifier. In a case of installing a new small-sized base station in a mobile communication system, the method and apparatus may set a code parameter, a time parameter, and a frequency parameter, differently from a neighboring small-sized base station using the cell identifier even when dedicatedly using a preamble in a contention-free scheme to avoid a collision of the preamble, so that a random access preamble may be managed without occurrence of the collision with the neighboring small-sized base stations.