He was born in Glasgow, the son of William Pagan and Margaret Maxwell.
In 1768 or 1769, he went to Falmouth Neck, Massachusetts (now Portland, Maine), where he became involved in the timber trade and ship building.
In October 1775, his premises were destroyed by American forces who were reacting to rebel activity in the area.
In 1780, Pagan settled at the mouth of the Penobscot River, believing that this would become a loyalist settlement, and established sawmills, stores and engaged in ship building.
He assisted in research and surveys which helped establish the St. Croix River as the international boundary with Maine.