An image reading apparatus which supports a both-side scan mode and a controlling method thereof. The image reading apparatus includes: an automatic paper transfer unit which automatically transfers a papers; a first scanning unit which comprises a first light source and scans a first side of the paper; a second scanning unit which comprises a second light source and scans a second side of the paper; and a controller which controls the first and second light sources to be alternately lit on a plurality of times within a cycle of a preset signal when the paper is transferred to the automatic paper transfer unit.