The Minangkabau from Sumatra settled in Negeri Sembilan in the 15th century under the protection of the Melaka Sultanate, and later under the protection of its successor, the Sultanate of Johor. As Johor weakened in the 18th century, attacks by the Bugis forced the Minangkabaus to seek protection from a prince from their homeland. The Minangkabau ruler, Sultan Abdul Jalil, obliged by sending his near relative, Raja Melewar. Arriving to find that a certain Raja Khatib had already established himself as ruler, Melewar was forced to compromise with the lesser chiefs in order to secure his position. He defeated Raja Khatib with their help, receiving Seri Menanti as his personal domain. The Sultan of Johor, confirmed his position by granting the title Yang di-Pertuan Besar Negeri Sembilan (He Who is Highest Lord of the Nine States) in 1773. After Raja Melewar's death, a series of disputes arose over the succession. For a considerable period, the local nobles applied to the Minangkabau ruler in Sumatra for a ruler. However, competing interests supported different candidates, often resulting in instability and civil war.
In 1873, the British intervened militarily in a civil war in Sungai Ujong to preserve British economic interests, and placed the country under the control of a British Resident. Jelebu followed in 1886, and the remaining states in 1895. In 1897, when the Federated Malay States (FMS) was established, Sungai Ujong and Jelebu were reunited to the confederation of small states and the whole, under the old name of the Negeri Sembilan, was placed under a single Resident and became a member of the FMS.
The number of states within Negeri Sembilan has fluctuated over the years, the federation now consists of six states and a number of sub-states under their suzerainty. The former state of Naning was annexed by Malacca, Kelang by Selangor, and Segamat by Johor.
Negeri Sembilan endured Japanese occupation in World War II between 1941 and 1945, and joined the Federation of Malaya in 1948, and became a state of Malaysia in 1963.
The current Yang di-Pertuan Besar is Tuanku Jaafar ibni Almarhum Tuanku Abdul Rahman, born 1922, who was elected in 1967. The current Menteri Besar or Chief Minister of the state is YAB Dato' Seri Utama Mohamad Haji Hasan.