The Jaffna Diocese of the Church of South India (JDCSI) is part of the wider Church of South India (CSI), an episcopal (bishop-led) church formed through a historic union of several Protestant traditions.

Christian mission work in Jaffna began with the arrival of the American Ceylon Mission in 1816, followed by the formation of organized church bodies such as the Ceylon Congregational Council (1905). Various Protestant missions—including Congregational, Presbyterian, and Reformed traditions—worked in South India and Ceylon.

In 1908, these groups initiated a union, which led to the formation of the South India United Church (SIUC) in 1910. The Jaffna Congregational Council became part of this united body as the Jaffna Council.

A major milestone occurred on 27 September 1947, when the Church of South India (CSI) was officially formed through the union of the SIUC, Methodist, and Anglican churches. As a result, the Jaffna Council became the Jaffna Diocese of the CSI.

Shortly after, on 20 October 1947, the American Ceylon Mission formally handed over its work to the Diocese, expanding its responsibilities.

Although the Jaffna church had originally followed a Congregational tradition, it became part of the episcopal structure of the CSI after the union.

Over time, the Diocese developed its governing constitution, with key publications and revisions in 1942, 1959, 1995, 2009, and 2016, aligning with the CSI Synod’s regulations.

Today, the Diocese operates under the authority of the CSI Constitution, with its administrative office located in Vaddukoddai, and its jurisdiction covering areas originally entrusted by the American Ceylon Mission.