Jogues was born on January 10, 1607, at Orléans, into a bourgeois family, who had him educated at home. In 1624, at the age of seventeen, he entered the Jesuit novitiate at Rouen, where his Master of novices was Louis Lallemant. The master already had two brothers and a nephew serving as missionaries in the colony of New France. Jogues professed simple vows in 1626, and was sent to study philosophy at the royal college in La Flèche. The Jesuit community running it had a strong missionary spirit; its teachers included missionary pioneers, Énemond Massé, and later Jean de Brébreuf, while the colony was in British hands. Upon completing these studies, Jogues was sent to the Collège de Clermont in Paris to pursue his study of theology.
Paul Le Jeune, superior of the Jesuit mission in Canada, had conceived the plan for keeping the church and laity informed of the mission's undertaking, by the careful compilation of missionaries' letters. These described in detail their experiences and impressions. Every summer, for a period of 40 years, the Jesuit missionaries sent these reports back to Paris, where they were published serially under the title of the Jesuit Relations. These accounts inspired Jogues to become a missionary.
Allowed to cut his studies short, Jogues was ordained a priest in January 1636, and was accepted for service in the missions and sent to New France. He was assigned as a missionary to the Huron and Algonquian allies of the French. He sailed from France on the following 8 April, arriving in the village of Quebec in late May. He celebrated his first Mass in the New World on 31 May. He proceeded to the settlement of Trois-Rivières, where he stayed several weeks until he was instructed to join the Superior of the Jesuit Mission, Jean de Brébeuf, at their settlement on Lake Huron. Arriving there on 11 September, he immediately fell ill, as did later the other Jesuits and then the people of the village. Due to recurring epidemics, the people of the village soon threatened to kill the missionaries, but the epidemics ended before any attacks took place.
In 1639, the new superior of the Jesuit Mission, Father Jérôme Lalemant, entrusted the building of Fort Sainte-Marie to Jogues. The younger man traveled with Garnier to the Petun, known as the Tobacco Nation for their chief commodity crop. In September 1641, Jogues and Charles Raymbaut went into the territory of the Sauteurs (Chippewa). They pushed on a considerable distance to the west and came to the Sainte-Marie Falls (Sault Ste. Marie). They were warmly welcomed, the meeting was a productive one, and the priests had to promise to come
back to teach the people of the Christian faith.
On 3 August 1642, while on his way by canoe to the country of the Huron, Jogues, in the company of Guillaume Couture, René Goupil, and several Huron Christians, was captured by a war party of Mohawk of the Iroquois Confederacy. The Mohawk took their captives to their village of Ossernenon (now Auriesville, New York) on the Mohawk River, about forty miles west of the present city of Albany, New York. They were ritually tortured and Jogues lost two fingers on his right hand.
Jogues survived this event and lived as a slave among the Mohawk for some time; he tried to teach his captors about Christianity. Some Dutch traders from Fort Orange (now Albany, New York) ransomed him and gave him money for passage down the Hudson River to New Amsterdam (New York) and a return to France. Jogues was the first Catholic priest to visit Manhattan Island. From there, he sailed back to France, where he was greeted with surprise and joy. As a "living martyr", Jogues was given a dispensation by Pope Urban VIII to say Mass with his mutilated hand. Under Church law of the time, the Blessed Sacrament could not be touched with any fingers but the thumb and forefinger. Jogues visited his mother in Orléans but was eager to return to the missions. Within a few months, he returned to New France to continue his work. In 1645, a tentative peace was forged between the Iroquois and the Huron, Algonquin, and French. In the spring of 1646, Jogues was sent back to the Mohawk country along with Jean de Lalande to act as ambassador among them. Some among the Mohawk regarded Jogues and other missionaries as evil practitioners of magic. When they suffered another crisis of infectious disease and crop failure at Ossernenon, they blamed it on the chest of vestments and books that the Jesuits had left behind. On October 18, 1646, Jogues was attacked with a tomahawk and died; LaLande was killed the next day. The Mohawk threw the missionaries' bodies into the Mohawk River.