The second son of Tuanku Abdul Rahman ibni Almarhum Tuanku Muhammad, he was the first of four children by his commoner wife, Eurasian nurse Dulcie Campbell or better known as Che' Engku Maimunah binti Abdullah. The couple subsequently divorced.
Tuanku Ja’afar was to have left for Japan to serve as the Malaysian Ambassador to that country but was recalled by the State Government of Negeri Sembilan following the demise of his half brother HRH Tuanku Munawir, the then ruler of Negeri Sembilan, in 1967.
All four Undang (Territorial Chiefs) had unanimously elected Tuanku Ja’afar as the Yang di-Pertuan Besar of Negeri Sembilan to succeed HRH Tuanku Munawir. The election was controversial as the heir presumptive to the throne, Tuanku Munawir's son Tunku Muhriz was by-passed. It has been suggested that the then Prime Minister of Malaysia, Tunku Abdul Rahman, instructed the council not to choose Tunku Muhriz on account of his youth (he was then eighteen).
Tuanku Ja’afar ascended the throne as the 10th Ruler of Negeri Sembilan on 18 April 1967.
Tuanku Ja’afar was the tenth Yang di-Pertuan Agong of Malaysia from 26 April 1994 until 25 April 1999 succeeding Sultan Azlan Shah of Perak.
Tuanku Ja’afar married Tuanku Najihah binti Almarhum Tunku Besar Burhanuddin of Negeri Sembilan who also served as his Raja Permaisuri Agong between 1994 and 1999. The royal couple are blessed with three sons and three daughters whose names are:-
- Tunku Naquiyuddin ibni Almarhum Tuanku Ja'afar;
- Tunku Imran ibni Almarhum Tuanku Ja'afar;
- Tunku Nadzaruddin ibni Almarhum Tuanku Ja'afar
- Tunku Naquiah binti Almarhum Tuanku Ja'afar;
- Tunku Jawahir binti Almarhum Tuanku Ja'afar;
- Tunku Irinah binti Almarhum Tuanku Ja'afar