Although the Lords Proprietors originally envisioned a single province with a single government, Carolina started out with separate governments for each county. All later attempts to consolidate these different groups failed completely.

On September 8, 1663, when the Lords Proprietors asked Sir William Berkeley, one of their own as well as the current sitting governor of Virginia, to appoint the first governor of "upper Carolina" - which soon became Albemarle County in 1664 - they also instructed that the governor should have a Council to help him guide the colony.

Upon his appointment circa October of 1664, Governor William Drummond was directed to appoint six men to be his Council and that he and this group of advisors would also constitute the "upper House" of a somewhat bicameral legislature to include a small House of Burgesses elected by the Freemen of the colony. At first, each member of the Council was to be appointed for a four year term, but their tenure would soon evolve to be "for life" unless they did something really heinous or really stupid. The names of the earliest Council members are not currently known.

On January 7, 1665 (one source asserts in was January 11th), John Yeamans was commissioned as governor of Clarendon County along the Cape Fear River. This short-lived county established a legislature and an Executive Council of six members in 1666, but was abandoned by August of 1667 due to utter destruction by a very large hurricane. None of the names of this short-lived Executive Council are currently known.

On July 26, 1669, the Lords Proprietors commissioned John Yeamans again as the "Governour of all that Territory, or part of the Province of Carolina that lies southward and westward of Cape Carteret." (Cape Carteret was later renamed to Cape Romain.) He sailed from England in January of 1670 in three ships with about 150 settlers, and they landed first at Bermuda, where Yeamans appointed William Sayle governor in his stead - Yeamans went on to Barbados. The 150 settlers with Gov. William Sayle first landed at Port Royal, then proceeded to the Ashley River and established the town of Charles Town at Albemarle Point in April of 1670. The Lords Proprietors named five deputies to accompany the first settlers of Charles Town and instructed the leaders that as soon as they reached Carolina the freemen should be called together and should elect five other deputies to be joined with those appointed by the Lords Proprietors to form what was to be called the Council.

With the issuance of the Fundamental Constitutions in 1669 and 1670, the Lords Proprietors authorized themselves to each have a "deputy" in Carolina. The Palatine's deputy would be the governor, and the seven (7) other Lords Proprietors' deputies would constitute his Executive Council and the "upper House" to serve in the Assembly. Although it was first imagined to be a single colony with a single government, from the very beginning there were separate governments in Albemarle County (starting in 1664), Clarendon County (1664-1667), then Craven County (i.e., Charles Town) in 1670. Each had their own Executive Council.

As each governor, deputy governor, and sometimes an elected President of the Executive Council upon the death of an appointed governor/deputy, were issued formal instructions from the Lords Proprietors, these instructions soon included the names of each of the Lords Proprietors' deputies and members of the Executive Council. There were infrequent times when a sitting governor would have to name new members of the Executive Council - due to prolongued absence or illness, or due to the death of a member of the Executive Council. In most cases, these named by the governor would soon thereafter be approved by the Lords Proprietors in London. In rare cases, the Lords Proprietors disapproved of an Executive Council member appointed by a governor.

When the Crown purchased Carolina from the Lords Proprietors in 1728/1729, they assumed the privilege of appointing all members of the Executive Councils in both North Carolina and South Carolina - and each colony was authorized to have twelve (12) members in the Executive Council. Whenever possible, the Crown discussed potential appointments to the Executive Council with new incoming governors.