Jowai's history is deeply intertwined with the legacy of the Jaintia Kingdom (also known as the Sutnga Kingdom), one of the oldest and most powerful kingdoms in the region before the arrival of the British. The indigenous Pnar people have inhabited these hills for centuries, developing a rich agrarian and trading society.
In the 19th century, the British East India Company began expanding into the region, formally annexing the Jaintia Hills in 1835 after a series of conflicts. The introduction of house taxes and interference in local religious customs sparked widespread resentment. This culminated in the Jaintia Rebellion (1860–1862), famously led by the legendary freedom fighter U Kiang Nangbah. A native of Jowai, Nangbah organized a fierce guerrilla war against the British before being captured and publicly hanged in the central market of Jowai (Iawmusiang) in 1862.
Following India's independence in 1947, the region was part of the state of Assam. In 1972, the autonomous state of Meghalaya was carved out, and Jowai became the headquarters of the newly formed Jaintia Hills district. In 2012, the district was bifurcated for better administration, establishing Jowai as the headquarters of the West Jaintia Hills district.