Provided is a method of manufacturing a thin film transistor that can improve self-alignment. In this method, a semiconductor layer comprising a first doped region, a second doped region and a channel region is formed on a sacrificial layer on a first substrate. Next, the semiconductor layer is separated from the first substrate and is then coupled on a second substrate. Next, a dielectric layer is formed on the second substrate and the semiconductor layer, and a first photoresist layer is formed on the dielectric layer. Thereafter, the first photoresist layer is exposed to light from a rear surface of the second substrate by using the first doped region and the second doped region as a mask, to form a first mask pattern. Next, a gate electrode overlapping the channel region is formed on the dielectric layer by using the first mask pattern as a mask, and a source electrode and a drain electrode connected to the first doped region and the second doped region, respectively are formed to complete a thin film transistor.