He was born in Buhy, now situated in Val-d'Oise. His mother had leanings toward Protestantism, but his father tried to counteract her influence by sending him to the Collège de Lisieux at Paris. On his father's death in 1559, however, the family formally adopted the reformed faith. Mornay studied law and jurisprudence at the University of Heidelberg in 1565 and the following year Hebrew and German at the University of Padua. During the French Wars of Religion in 1567, he joined the army of Louis I de Bourbon, prince de Condé, but a fall from his horse prevented him from taking an active part in the campaign. His career as Huguenot apologist began in 1571 with the work Dissertation sur l'Église visible, and, as a diplomat in 1572, he undertook a confidential mission for Admiral de Coligny to William the Silent, Prince of Orange.
He escaped the St. Bartholomew's Day Massacre by the aid of a Catholic friend, taking refuge in England. Returning to France towards the end of 1573, he participated during the next two years with various success in the campaigns of the future Henry IV of France, then only King of Navarre. He was taken prisoner by the Duke of Guise on 10 October 1575 was but ransomed for a small sum, which was paid by Charlotte Arbaleste, whom he married shortly afterwards at Sedan.
Mornay was gradually recognized as Henry's right-hand man, representing him in England from 1577 to 1578 and again in 1580, and in the Low Countries 1581-1582. With the death of the Duke of Alençon-Anjou in 1584, by which Henry was brought within sight of the throne of France, the period of Mornay's greatest political activity began, and after the death of Henry I, Prince of Condé, in 1588, his influence became so great that he was popularly styled the "Huguenot pope". He was present at the siege of Dieppe, fought at Ivry, and was at the siege of Rouen in 1591-92 until he sent on a mission to the court of Queen Elizabeth. Both he and his wife befriended English Protestants like Francis Walsingham, Mary Sidney, and her brother Philip Sydney.
He was bitterly disappointed by Henry IV's abjuration of Protestantism in 1593 and gradually withdrew from the court, devoting himself to the Academy of Saumur, which had a distinguished history until its suppression by Louis XIV in 1683.
His last years were saddened by the loss of his only son in 1605 and that of his devoted wife in 1606, but he spent them in perfecting the Huguenot organization. He was chosen a deputy in 1618 to represent the French Protestants at the Synod of Dort. He was prohibited from attending by Louis XIII but contributed materially to its deliberations by written communications. He lost the governorship of Saumur at the time of the Huguenot insurrection in 1621 as Saumur was captured by French royal forces, and died in retirement on his estate of La Forêt-sur-Sèvre, Deux-Sèvres.