He was married to his full sister Isetemkheb D (both children of Menkheperre, the High Priest of Amun at Thebes, by Isetemkheb III, hence both nephew, niece and grandchildren of Psusennes I and also to his niece Nesikhons, the daughter of his brother Smendes II.

[3] When Pinedjem II died, his mummy, along with those of his wives and at least one daughter, Nesitanebetashru, were interred in the tomb DB320 at Deir el-Bahri, above the Mortuary Temple of Hatshepsut.

Subsequently, the mummies of other previous Theban-based rulers, including the much earlier New Kingdom pharaohs Ahmose I, Amenhotep I, Thutmose II, Thutmose III, Ramesses I, Seti I, Ramesses II, and Ramesses IX were gathered together and also laid in this tomb, which was revealed in 1881.

This was done to prevent their remains from being robbed as their graves have been looted by many ancient tomb raiders.

Pinedjem II was a contemporary of the Egyptian king Siamun with Pinedjem II controlling Upper Egypt and Siamun ruling over Lower Egypt.