Six-year-old Yaakov Dov Shrot was found in the Arab town of Hizme just north of Jerusalem on Monday morning by emergency rescue services.
Previously, authorities had expressed concern over whether or not Shrot was indeed still alive.
He does not seem to have been harmed or ill.
Shrot, who is autistic, went missing on Sunday afternoon. He had last been seen getting off the bus with his father in the Jerusalem neighborhood of Neve Yaakov. According to the father, the boy ran off and went missing soon afterwards.
United Hatzalah psycho-trauma unit director Miriam Ballin said, "Yaakov is known for his energy and curiosity. We are hoping that the same energy and curiosity that got him into this mess will help him be found."