Johor Bahru was founded in the late 1850's by the father of Sultan Abu Bakar, one of the most best-remembered of all Malay Sultans (traditional Malay kings or rulers).  The town was first called Tanjung Puteri and it was a small Malay fishing village.  Sultan Abu Bakar changed the name to Johor Bahru when he proclaimed it the capital of his kingdom in 1866, following the act of moving the seat of the government from the old capital at Teluk Belanga (now Johor Lama) on Sungai Johor (Johor River).

Descended from the legendary Temenggong Abdul Rahman, a local chief who signed the initial treaty with the British when they sought permission to lease Singapore island in 1819, Sultan Abu Bakar was one of the most competent of all the Sultans who have ruled the Malay States.   Much of the prosperity Johor enjoys today can be traced directly to his success in persuading British and Chinese entrepreneurs to invest in agricultural estates in his Sultanate.  He was widely respected for his business and political acumen, as well as his sense of justice.  On several occasions he acted as an intermedian between other Malay Sultans and the British.  Sultan Abu Bakar took a great interest in planning and laying out his royal city of Johor Bahru; consequently, much of the city today bears his name and marks.  For example, the Bangunan Sultan Abu Bakar (State Secretariat Building), Royal Abu Bakar Museum and Sultan Abu Bakar Mosque.

Johor Bahru has witnessed a few major Malaysian historical events such as the establishment of UMNO (United Malays National Organisation) in the 1950s, which is currently the leading political party in Malaysia.

More recently, the council that manages Johor Bahru was officially promoted to Johor Bahru City Council from Johor Bahru Municipal Council on January 1st, 1994.  To commemorate the proclamation, the State Government of Johor build a clock tower named Dataran Bandaraya (City Square) with one of the largest clock in South East Asia.  Dataran Bandaraya is now the official landmark for the City.