The history of Mokokchung is intimately tied to the Ao Naga tribe, who have inhabited the region for centuries. According to oral traditions, the Ao people migrated from places like Chungliyimti to the present-day Mokokchung area. The area originally consisted of large, fortified hilltop villages governed by traditional tribal councils.
The modern township began to take shape in 1890 when the British colonial administration established Mokokchung as a subdivision of the Naga Hills district. This move was strategic, aimed at extending British influence into the interior Naga territories. A few years later, in 1894, American Baptist missionaries established a mission centre in nearby Impur. This centre brought formal education, the printing press, and Christianity to the region, fundamentally transforming the cultural and intellectual landscape of Mokokchung.
When Nagaland was granted statehood in 1963, Mokokchung was one of the state's three original districts (alongside Kohima and Tuensang). Throughout the mid-to-late 20th century, the city played a pivotal role in the Naga nationalist movement and the subsequent socio-political developments of the state. Today, it stands as a testament to the resilience of its people, successfully marrying its rich tribal heritage with modern educational and economic progress.