Joko was the son of Ki Ageng Pengging, born as Mas Karèbèt.

When he was conceived, his father was having a wayang beber (shadow puppet) show performed by the dalang Ki Ageng Tingkir.

Ten years later, Ki Ageng Pengging was sentenced to capital punishment for rebellion against the Sultanate of Demak with Sunan Kudus as the executioner.

After her husband's execution, Nyai Ageng Pengging also fell ill and died.

He followed the teaching of Sunan Kalijaga as well as Ki Ageng Sela.