The appendix to Common Sense first appeared in the second edition of the pamphlet, published on February 14, 1776. It is not considered part of the original work; rather than being part of his detailed argument for independence, the appendix lays out a few of Paine's arguments and responds to concerns of the day. The first of the appendix's two parts recaps many of the arguments Paine makes in Common Sense, although the style of writing is a bit more urgent. The main points that come out of the first part of the appendix are as follows: the colonies should immediately declare independence; independence is preferable to reconciliation because it is simpler; independence is the only bond that can keep the colonies together.

The second part of the appendix, "To the Representatives of the Quakers," replies to a number of points raised by some Quaker leaders concerning the American Revoluion. Paine begins by proclaiming his religious toleration and his faith in God. He criticizes the Quaker writers for meddling in political matters and for presenting themselves as representative of the entire Quaker populace. Paine says he will be equally presumptuous in his writing in order to get the Quaker authors to understand the foolishness of their position.

Paine then voices his agreement with the principles of love and peace that the Quaker authors expressed in their writing. He writes that he wishes to establish an everlasting and stable peace, which can only be established through a complete separation of the colonial states from Britain. Paine adds that the revolution is being fought in defense, as the British are attacking the colonials on their own soil. With no legal means of resolving the matter, the colonials have no choice but to fight and defend themselves, and the Quaker attack on the colonials for bearing arms is therefore unfair. Paine says the Quakers should channel their disapproval against the British for beginning the battle, and that the colonials cannot be condemned for self-defense. Rather than directing their preaching against the colonists, the Quakers should condemn the king for his misdeeds and tell him to repent.

Paine considers a biblical passage from Proverbs invoked by the Quakers: "when a man's ways please the Lord, he maketh even his enemies to be at peace with him." This passage, Paine argues, only serves to prove that the English king's ways do not please the Lord, because if they did, than the American colonists would be at peace instead of revolting.

Paine considers the Quaker perspective that governments are God's business, and that they aim to live a peaceful life under whatever government God gives them. If the Quakers believe what they have written, Paine argues, then there is no room for their political involvement at all. They should simply wait and see whether God wants the revolution to succeed or not, and then follow whichever government is left in power at the end. Paine further ridicules this general principle, arguing that if it were true that governments were God's business, then no man could be held accountable or condemned for overthrowing a king.

Paine concludes with a condemnation "of mingling religion and politics," and the hope that such mingling "may be disavowed and reprobated by every inhabitant of America."