He was born at Agen, the tenth child and third son of Italian scholar Julius Caesar Scaliger and Andiette de Roques Lobejac. When he was twelve years old, he was sent with two younger brothers to the College of Guienne in Bordeaux, which was then under the direction of Jean Gelida. An outbreak of the plague in 1555 caused the boys to return home, and for the next few years Joseph was his father's constant companion and amanuensis.

The composition of Latin verse was the chief amusement of his father Julius in his later years, and he would daily dictate to his son between eighty and a hundred lines, and sometimes even more. Joseph was also required each day to write a Latin theme or declamation, though in other respects he seems to have been left to his own devices. He learned from his father to be not only a scholar, but also an acute observer, aiming at historical criticism more than at correcting texts.

After his father's death he spent four years at the University of Paris, where he began the study of Greek under Adrianus Turnebus. But after two months he found he was not in a position to profit from the lectures of the greatest Greek scholar of the time. He read Homer in twenty-one days, and then went through all the other Greek poets, orators and historians, forming a grammar for himself as he went along. From Greek, at the suggestion of Guillaume Postel, he proceeded to attack Hebrew, and then Arabic; of both he acquired a respectable knowledge.

His most important teacher was Jean Dorat. He was able not only to impart knowledge, but also to kindle enthusiasm. It was to Dorat that Scaliger owed his home for the next thirty years of his life, for in 1563 the professor recommended him to Louis de Chastaigner, the young lord of La Roche - Posay, as a companion in his travels. A close friendship sprang up between the two young men, which remained unbroken till the death of Louis in 1595. The travellers first went to Rome. Here they found Marc Antoine Muretus, who, when at Bordeaux and Toulouse, had been a great favourite and occasional visitor of Julius Caesar Scaliger at Agen. Muretus soon recognized the young Scaliger's merits, and introduced him to many contacts well worth knowing.

After visiting a large part of Italy, the travellers moved on to England and Scotland, passing as it would seem La Roche - Posay on their way. Scaliger formed an unfavourable opinion of the English. Their inhuman disposition and inhospitable treatment of foreigners especially made a negative impression on him. He was also disappointed in finding only few Greek manuscripts and few learned men. It was not until a much later period that he became intimate with Richard Thomson and other Englishmen. In the course of his travels he had become a Protestant.

On his return to France he spent three years with the Chastaigners, accompanying them to their different châteaux in Poitou, as the calls of the civil war required. In 1570 he accepted the invitation of Jacques Cujas and proceeded to Valence to study jurisprudence under the greatest living jurist. Here he remained three years, profiting not only by the lectures but even more by the library of Cujas, which filled no fewer than seven or eight rooms and included five hundred manuscripts.

The massacre of St Bartholomew — occurring as he was about to accompany the bishop of Valence on an embassy to Poland — made Scaliger flee, together with other Huguenots, for Geneva, where he was appointed a professor in the academy. He lectured on the Organon of Aristotle and the De Finibus of Cicero to much satisfaction for the students, but not appreciating it himself. He hated lecturing, and was bored with the importunities of the fanatical preachers; and in 1574 he returned to France and made his home for the next twenty years with Chastaigner.

Of his life during this period we have interesting details and notices in the Lettres françaises inédites de Joseph Scaliger, edited by Tamizey de Larroque (Agen, 1881). Constantly moving through Poitou and the Limousin, as the exigencies of the civil war required, occasionally taking his turn as a guard, at least on one occasion trailing a pike on an expedition against the Leaguers, with no access to libraries, and frequently separated even from his own books, his life during this period seems most unsuited to study. He had, however, what so few contemporary scholars possessed — leisure, and freedom from financial cares.

It was during this period of his life that he composed and published his books of historical criticism. His editions of the Catalecta (1575), of Festus (1575), of Catullus, Tibullus and Propertius (1577), are the work of a man determined to discover the real meaning and force of his author. He was the first to lay down and apply sound rules of criticism and emendation, and to change textual criticism from a series of haphazard guesses into a "rational procedure subject to fixed laws" (Mark Pattison).

But these works, while proving Scaliger's right to the foremost place among his contemporaries as Latin scholar and critic, did not go beyond mere scholarship. It was reserved for his edition of Manilius (1579), and his De emendatione temporum (1583), to revolutionize perceived ideas of ancient chronology — to show that ancient history is not confined to that of the Greeks and Romans, but also comprises that of the Persians, the Babylonians and the Egyptians, hitherto neglected, and that of the Jews, hitherto treated as a thing apart; and that the historical narratives and fragments of each of these, and their several systems of chronology, must be critically compared. It was this innovation that distinguished Scaliger from contemporary scholars. Neither they nor those who immediately followed seem to have appreciated his innovation. Instead, they valued his emendatory criticism and his skill in Greek. His commentary on Manilius is really a treatise on ancient astronomy, and it forms an introduction to De emendatione temporum, In this work Scaliger investigates ancient systems of determining epochs, calendars and computations of time. Applying the work of Nicolaus Copernicus and other modern scientists, he reveals the principles behind these systems.

In the remaining twenty-four years of his life he expanded on his work in the De emendatione. He succeeded in reconstructing the lost Chronicle of Eusebius — one of the most valuable ancient documents, especially valuable for ancient chronology. This he printed in 1606 in his Thesaurus temporum, in which he collected, restored, and arranged every chronological relic extant in Greek or Latin.

When in 1590 Justus Lipsius retired from the University of Leiden, the university and its protectors, the States - General of the Netherlands and the prince of Orange, resolved to appoint Scaliger his successor. He declined; he hated lecturing, and there were those among his friends who erroneously believed that with the success of Henry IV learning would flourish, and Protestantism would be no barrier to his advancement. The invitation was renewed in the most flattering manner a year later; the invitation stated Scaliger would not be required to lecture, and that the university only wished for his presence, while he would be able to dispose of his own time in all respects. This offer Scaliger accepted provisionally. Midway through 1593 he set out for the Netherlands, where he would pass the remaining thirteen years of his life, never returning to France. His reception at Leiden was all that he could have wished for. He received a handsome income; he was treated with the highest consideration. His supposed rank as a prince of Verona (a sensitive issue for the Scaligeri) was recognized. Leiden being midway between The Hague and Amsterdam, Scaliger was able to enjoy, besides the learned circle of Leiden, the advantages of the best society of both these capitals. For Scaliger was no hermit buried among his books; he was fond of social intercourse and was himself a good talker.

During the first seven years of his residence at Leiden his reputation was at its highest point. His literary judgement was unquestioned. From his throne at Leiden he ruled the learned world; a word from him could make or mar a rising reputation, and he was surrounded by young men eager to listen to and profit from his conversation. He encouraged Grotius when only a youth of sixteen to edit Capella. At the early death of the younger Douza he wept as at that of a beloved son. Daniel Heinsius, at first his favourite pupil, became his most intimate friend.

At the same time, Scaliger had made numerous enemies. He hated ignorance, but he hated still more half - learning, and most of all dishonesty in argument or in quotation. Himself the soul of honour and truthfulness, he had no toleration for the disingenuous argument and the misstatements of facts of those who wrote to support a theory or to defend an unsound cause. His pungent sarcasm soon reached the ears of the persons who were its object, and his pen was not less bitter than his tongue. He was conscious of his power, and not always sufficiently cautious or sufficiently gentle in its exercise. Nor was he always right. He trusted much to his memory, which was occasionally treacherous. His emendations, if often valuable, were sometimes absurd. In laying the foundations of a science of ancient chronology he relied sometimes on groundless or even absurd hypotheses, often based on an imperfect induction of facts. Sometimes he misunderstood the astronomical science of the ancients, sometimes that of Copernicus and Tycho Brahe. And he was no mathematician.

But his enemies were not merely those whose errors he had exposed and whose hostility he had excited by the violence of his language. The results of his method of historical criticism threatened the Catholic controversialists and the authenticity of many of the documents on which they relied. The Jesuits, who aspired to be the source of all scholarship and criticism, saw the writings and authority of Scaliger as a formidable barrier to their claims. Muretus in the latter part of his life professed the strictest orthodoxy, Lipsius had been reconciled to the Church of Rome, Isaac Casaubon was supposed to be wavering, but Scaliger was known to be an irreconcilable Protestant. As long as his intellectual supremacy was unquestioned, the Protestants had the advantage in learning and scholarship. His enemies therefore aimed, if not to answer his criticisms or to disprove his statements, yet to attack him as a man and to destroy his reputation. This was no easy task, for his moral character was strong.

After several scurrilous but ineffectual attacks by the Jesuit party, in 1607 a new and more successful attempt was made. Scaliger's weak point was his pride. In 1594 Scaliger had published his Epistola de vetustate et splendore gentis Scaligerae et JC Scaligeri vita. In 1601 Gaspar Scioppius, then in the service of the Jesuits published his Scaliger hypototimaeus ("The Supposititious Scaliger"), a quarto volume of more than four hundred pages, written with consummate ability in an admirable and incisive style, with the entire disregard for truth which Scioppius always displayed, and with all the power of his accomplished sarcasm. Every piece of scandal which could be raked together concerning Scaliger or his family is to be found there. The author professes to point out five hundred lies in the Epistola de vetustate of Scaliger, but the main argument of the book is to show the falsity of his pretensions to be of the family of La Scala, and of the narrative of his father's early life. "No stronger proof," says Pattison, "can be given of the impressions produced by this powerful philippic, dedicated to the defamation of an individual, than that it had been the source from which the biography of Scaliger, as it now stands in our biographical collections, has mainly flowed."

To Scaliger the blow was crushing. Whatever his father Julius had believed, Joseph had never doubted to be a prince of Verona, and in his Epistola had put forth with the most perfect good faith, and without inquiry, all that he had heard from his father. He immediately wrote a reply to Scioppius, entitled Confutatio fabulae Burdonum. It is written, for Scaliger, with unusual moderation and good taste, but perhaps for that very reason had not the success which its author wished and even expected. In the opinion of Pattison, "as a refutation of Scioppius it is most complete"; but there are certainly grounds for dissenting from this judgment. Scaliger undoubtedly shows that Scioppius committed more blunders than he corrected, that his book literally bristles with pure lies and baseless calumnies; but he does not succeed in adducing a single proof either of his father's descent from the La Scala family, or of any single event narrated by Julius as happening to himself or any member of this family prior to his arrival at Agen. Nor does he even attempt a refutation of the crucial point, which Scioppius had proved, as far as a negative can be proved, namely, that William, the last prince of Verona, had no son Nicholas, who would have been the alleged grandfather of Julius.

But whether complete or not, the Confutatio had no success; the attack of the Jesuits was successful, far more so than they could possibly have hoped. Scioppius was wont to boast that his book had killed Scaliger. It certainly embittered the few remaining months of his life, and it is not improbable that the mortification which he suffered may have shortened his days. The Confutatio was his last work. Five months after it appeared, on January 21, 1609, at four in the morning, he died in the arms of his son Heinsius. In his will Scaliger bequeathed his renowned collection of manuscripts and books (tous mes livres de langues étrangères, Hebraiques, Syriens, Arabiques, Ethiopiens) to Leiden University Library.