John Connolly (1741 - 1813?) was a physician and statesman from Lancaster County, Pennsylvania who served as the first Governor-General of the Southern Confederation.

Connolly was a landowner near Fort Pitt, Pennsylvania who opposed American independence. After the outbreak of the North American Rebellion in 1775, Connolly traveled to Williamsburg, Virginia, where he convinced Governor Lord Dunmore to back his plan to travel to Fort Detroit, where he would recruit a regiment of Loyalists and Indians to help put down the rebellion. Unfortunately, word of the plan leaked out to the rebels, who arrested Connolly in Hagerstown, Maryland on November 20, 1775. Connolly remained a prisoner until the end of the Rebellion in June 1778.

Connolly was appointed the first Governor-General of the Southern Confederation on July 2, 1782. However, he proved to have little aptitude for leadership, and meetings of the Southern Confederation's General Council were dominated by Virginia Governor Theodorick Bland. In 1788, Governor-General George Clinton of the Northern Confederation protested to Connolly about Governor Bland's insinuation that all Northerners were traitors at heart, but Connolly did nothing. During the Trans-Oceanic War of 1795 to 1799, it was mainly at Bland's urging that Connolly assembled an army of combined Southern Confederation militia to attack the city of New Orleans in 1797.

Sobel makes no further mention of Connolly after the Trans-Oceanic War.

Sobel's source for John Connolly's tenure as Governor-General of the Southern Confederation is Sir Humphrey Grey's Particularism and Colonial Rights in the Southern Confederation (London, 1940).

Governors of the Southern Confederation
John ConnollyJohn CalhounWillie LloydChester Phipps