He was the eldest son of Pierre Hotman, and was born at Paris, his family being of Silesian origin. Pierre, a zealous Catholic and a counsellor of the parlement of Paris, intended his son for the law, and sent him at the age of fifteen to the University of Orléans. He obtained his doctorate in three years, and returned to Paris. The work of a barrister was not to his taste; he turned to jurisprudence and literature, and in 1546 was appointed lecturer in Roman Law at the University of Paris. The fortitude of Anne Dubourg under torture gained his adhesion to the cause of Reform.
Giving up a career on which he had entered with high repute, he went in 1547 to Lyons, and thence to Geneva and to Lausanne, where, on the recommendation of John Calvin, he was appointed professor of belles.-lettres and history, and married Claudine Aubelin, a refugee from Orléans. On the invitation of the magistracy, he lectured at Strasbourg on law in 1555, and became professor in 1556, superseding François Baudouin, who had been his colleague in Paris.
His fame was such that overtures were made to him by the courts of Prussia and Hesse, and by Elizabeth I of England. Twice he visited Germany, in 1556 accompanying Calvin to the diet of Frankfurt. He was entrusted with confidential missions from the Huguenot leaders to German potentates, carrying at one time credentials from Catherine de Medici. In 1560 he was one of the principal instigators of the conspiracy of Amboise; in September of that year he was with Antoine of Navarre at Nérac. In 1562 he attached himself to Condé. In 1564 he became professor of civil law at Valence, retrieving by his success the reputation of its university. In 1567 he succeeded Jacques Cujas in the chair of jurisprudence at Bourges.
Five months later his house and library were wrecked by a Catholic mob; he fled by Orléans to Paris, where Michel de l'Hôpital made him historiographer to the king. As agent for the Huguenots, he was sent to Blois to negotiate the peace of 1568. He returned to Bourges, but was driven away by the outbreak of hostilities. At Sancerre, during its siege, he composed his Consolatio (published in 1593). The peace of 1570 restored him to Bourges, whence a third time he fled the massacre of St Bartholomew (1572). In 1573, after publishing his Franco-Gallia, he left France for ever with his family, and became professor of Roman law at Geneva. On the approach of the duke of Savoy he removed to Basel in 1579. In 1580 he was appointed councillor of state to Henry of Navarre. The plague sent him in 1582 to Montbéliard, where his wife died. Returning to Geneva in 1584 he developed a kind of scientific turn, dabbling in alchemy and the research for the philosopher's stone. In 1589 he finally retired to Basel, where he died, leaving two sons and four daughters; he was buried in the cathedral.
Hotman was a home-loving and genuinely pious man (as his Consolatio shows). His constant removals were inspired less by fear for himself than for his family, and he had a constitutional desire for peace. He did much for 16th-century jurisprudence, having a critical knowledge of Roman sources, and a fine Latin style. He broached the idea of a national code of French law. His works were very numerous, beginning with his De gradibus cognationis (1546), and including a treatise on the Eucharist (1566); a treatise (Anti-Tribonien, 1567) to show that French law could not be based on Justinian; a life of Coligny (1575); a polemic (Brutum fulmen, 1585) directed against a bull of Sixtus V, with many other works on law, history, politics and classical learning.
His most important work, the Franco-Gallia (1573), was in advance of his age, and found favour neither with Catholics nor with Huguenots in its day; yet its vogue has been compared to that obtained later by Jean-Jacques Rousseau's Contrat Social. It presented an Ideal of Protestant statesmanship, pleading for a representative government and an elective monarchy. It served the purpose of the Jesuits in their pamphlet war against Henry IV of France.