A handheld electronic device comprising a main body, a stylus and a non-contact sensor is provided. The main body has a containing slot, and the stylus having a sensing region is suitable for being inserted into the containing slot. The non-contact sensor is disposed beside the containing slot. The non-contact sensor outputs a sensing signal for identifying the position of the stylus when the stylus moves in the containing slot and the sensing region of the stylus passes the non-contact sensor. By detecting the position of the stylus in a non-contact manner, the reliability and the lifetime of the handheld electronic device are improved, and a higher sensing precision is also provided.