A president and a nine-member council (representing the four towns of Portsmouth, Dover, Hampton and Exeter) were appointed by the king from the 4,000 settlers of the seacoast area and were required to assume office by January 21, 1680.

Some of the designated council members were so firmly opposed to the new government that they considered refusing their appointed positions.

John Cutt, a wealthy Portsmouth merchant, was appointed the first president (later called Governor) of New Hampshire.

The first official act of the President and Council was to create a legislative body, then called an Assembly, to raise taxes and establish public conduct laws.

They promptly enacted a law that New Hampshire's property owners' titles, as granted by the Massachusetts Bay Colony over the years, would continue as valid, contrary to the ruling of the King.

At that time, the council's primary responsibility was to report on the activities of the president to the King, especially if he strayed from the crown's dictates.

On January 5, 1776, the founding fathers of the state created New Hampshire's first constitution, which eliminated the position of governor, but kept the concept of a council due to its former status as a check on the power of authoritarian rule, a recurring theme during the Revolution and afterwards with the creation of the Articles of Confederation, an ethos that made the founding fathers change selection of councilors from appointed to elected positions In the second and current Constitution, first written in 1784, a head executive was renewed, but given the title "President" rather than Governor to avoid the connotations of the royal governorship during the colonial period.

The only time the council was in danger of being eliminated was in 1850, when the future U.S. President Franklin Pierce suggested its removal during that year's Constitutional Convention, with the voters of New Hampshire disagreeing with him by a more than two to one margin (27,910 to 11,299).

This was part of a massive Democratic landslide in which the party won control of both chambers of the New Hampshire General Court, the re-election of John Lynch as governor, and both of the state's seats in the federal U.S. House of Representatives.