Originally the Indian settlement of Pon Pon, the town of Jacksonborough took its name for John Jackson who was granted land along the Edisto River in 1701. Around 1735, it was recognized as a settlement, and a plan of the town drawn in 1780 shows 113 town lots. Jacksonborough became the county seat with a courthouse and jail. The first free school was established in Jacksonborough in 1744, and early Methodist and Episcopal churches were built.

In February 1782, with Charleston under siege by the British, the General Assembly met in Jacksonborough. The Masonic Lodge building and a tavern owned by Peter DuBose were used for the meetings of the Senate and the House. Thus, Jacksonborough became the Provisional Capital of South Carolina.

A post office was established in Jacksonboro on February 23, 1823. Its name was changed to "Jacksonborough" after July of 1869, and back again to Jacksonboro on November 28, 1892.

The South Carolina Gazette was published in the spring of 1782 at Parker's Ferry, a few miles above Jacksonboro, being the first publication outside Charleston.

A railroad was later built from Jacksonboro through Walterboro to Green Pond, where passengers caught another train to Charleston or Savannah. Francis Y. Glover was one of the early railroad stock-holders.

On the eighth of January, 1782, the British were in firm control of Charles Town, which they had captured in May, 1780. That same day, a mere thirty miles westward, the General Assembly of South Carolina’s Revolutionary government convened in their capitol, Jacksonboro, little more than a settlement on the Edisto River. By February 26th, they had formulated and passed several Confiscation Acts. The lists of names – some of them misspelled – accompanying the Acts were printed in the March 20, 1782 issue of Charlestown’s Royal Gazette. The list would be revised several times by time the war was over.

Jacksonboro was the county seat of Colleton County from 1799 to 1822. While Charleston was under siege in the American Revolution, Jacksonboro was named the provisional capital of South Carolina. During session held by the South Carolina Legislature from January to February 1782 at the Masonic Lodge and Tavern, the Confiscation and Amercement Acts were passed.