He was born in Verchères, Lower Canada in 1823, grew up in Laprairie and studied at the Petit Séminaire de Montréal. His uncle was Ludger Duvernay, Patriote and publisher of La Minerve. Fortin graduated from McGill College in medicine in 1845 and practiced at Laprairie. He helped treat patients during the typhus epidemic of 1847-48 at Grosse-Île. In 1849, he led a group of mounted constables that controlled riots after the passing of the Rebellion Losses Bill. From 1852 to 1867, he served as magistrate protecting fisheries in the Gulf of Saint Lawrence. Fortin also served as customs agent in the Gulf and, with his ship, La Canadienne, was the sole guardian of law and order in this region. During this period, Fortin also published a list of fish found in the Gulf region and prepared descriptions of marine mammals found there.
In 1867, he was elected to the federal and provincial legislatures for Gaspé. He was named commission of crown lands in the provincial executive council but resigned in 1874 after a scandal implicating the party in power. In the same year, he resigned from federal politics after it became illegal to hold seats in both houses. In 1875, he was named speaker for the provincial assembly; he was forced to resign in 1876 after allegations of improper procedures in his election. Although he was later exonerated, a replacement had already been chosen. While in office, he helped promote the development of the Baie de Chaleur Railway, telegraph service connecting the Gaspé peninsula to the rest of the province and the installation of lighthouses in the region. Fortin also helped to establish formal education in navigation in Canada. He opposed reciprocity with the United States and was a strong defender of Canadian fishing rights. He helped found the Société de Géographie de Québec and served as its first president.
He died in Laprairie in 1887, while still a member of the Senate.
In 2002, the Quebec Ministère des Ressources naturelles et de la Faune named a wildlife reserve on the Richelieu River after Pierre-Étienne Fortin.