In the 16th century AD, Sultan Ahmad and his followers left Melaka because they were attacked by the Portuguese and settled in Pagoh.

On the way to Penarikan in the middle of the road, by the riverbed, in a big wooden tree, Datuk Bendahara Paduka Tuan (The Treasurer of Melaka) sat leaning on the wooden banir facing the hollow in front of him, Sultan Ahmad and his father were not far from there, they together stopped being tired and rested for two days.

While sitting, Datuk Bendahara threw his hands around to get rid of the numbness and then he reached a piece of stone which he then hit.

Buyong Adil in his book "Sejarah Alam Melayu" wrote that Segamat is one of the 9 states that became a part of Negeri Sembilan as a result of the above events.

Segamat was then seceded to Johor by the British, along with Ulu Pahang (Bera and Temerloh) to Pahang, Beranang (Kajang, Semenyih and Hulu Langat) and Klang (Sepang and Kuala Langat) to Selangor excluding Lukut which is now part of Port Dickson.

The Johor branch campus of Universiti Teknologi MARA was constructed at Jementah in the end of the 1980s and started its operation in 1991.

The construction of UiTM campus in Segamat district turned Segamat into another important educational hub in Johor besides Skudai, which houses Universiti Teknologi Malaysia, Parit Raja which houses Universiti Tun Hussein Onn Malaysia (UTHM) and Pagoh which is the home to the Pagoh EduHub comprising UTHM, International Islamic University of Malaysia (IIUM), Politeknik Tun Syed Nasir Syed Ismail (PTSN) and Institut Kemahiran Belia Negara Pagoh.

Segamat experienced floods during the 1950s, 1984, 18 December 2006 and most recently 2 March 2023, which was caused by 3–4 days of nonstop rain.