Provided are a navigation system having a function of branch road guidance based on a running road, and a method thereof. The system includes a global positioning system (GPS) module, a map database (DB), a storage unit, a voice processor, and a controller. The GPS module measures a self position. The map DB stores map data comprising road information having a road guide code and an exit code. The storage unit stores road guide codes and exit codes for the running road and a branch road, and stores road guidance voice data, voice data on the branch road, and numeric voice data. The voice processor receives and combines the voice data, and generates and synthesizes branch road guidance voice data. The controller reads the road guide codes for the running road of the measured position and the branch road, and outputs the voice data.