Scaliger's father, Benedetto Bordone, was a miniaturist and illuminator. Scaliger himself was known in his youth by the family name Bordone, but later insisted that he was a scion of the house of La Scala, for a hundred and fifty years lords of Verona, and was born in 1484 at the Rocca di Riva, on Lake Garda. When he was twelve, his kinsman the emperor Maximilian placed him among his pages. He remained for seventeen years in the service of the emperor, distinguishing himself as a soldier and as a captain. But he was unmindful neither of letters, in which he had the most eminent scholars of the day as his instructors, nor of art, which he studied with considerable success under Albrecht Dürer.

In 1512 at the Battle of Ravenna, where his father and elder brother were killed, he displayed prodigies of valour, and received the highest honours of chivalry from his imperial cousin, who conferred upon him with his own hands the Order of the Golden Spur, augmented with the collar and the eagle of gold. But this was the only reward he obtained.

He left the service of Maximilian, and after a brief employment by another kinsman, the duke of Ferrara, he decided to quit the military life, and in 1514 entered as a student at the University of Bologna. He determined to take holy orders, in the expectation that he would become cardinal, and then pope, when he would wrest from the Venetians his duchy of Verona, of which the republic had despoiled his ancestors. But, though he soon gave up this design, he remained at the university until 1519.

The next six years he passed at the castle of Vico Nuovo, in Piedmont, as a guest of the Della Rovere, at first dividing his time between military expeditions in the summer, and study, chiefly of medicine and natural history, in the winter, until a severe attack of rheumatic gout brought his military career to a close.

Henceforth his life was wholly devoted to study. In 1525 he accompanied Antonio della Rovera, bishop of Agen, to that city as his physician. Such is the outline of his own account of his early life.

It was not until some time after his death that the enemies of his son first alleged that he was not of the family of La Scala, but was the son of Benedetto Bordone, an illuminator or schoolmaster of Verona; that he was educated at Padua, where he took the degree of M.D.; and that the story of his life and adventures before arriving at Agen was a tissue of fables. It certainly is supported by no other evidence than his own statements, some of which are inconsistent with well-ascertained facts.

The remaining thirty-two years of his life were passed almost wholly at Agen, in the full light of contemporary history. They were without adventure, almost without incident, but it was in them that he achieved so much distinction that at his death in 1558 he had the highest scientific and literary reputation of any man in Europe. A few days after his arrival at Agen he fell in love with a charming orphan of thirteen, Andiette de Roques Lobejac. Her friends objected to her marriage with an unknown adventurer, but in 1528 he had obtained so much success as a physician that the objections of her family were overcome, and at forty-five he married Andiette, who was then sixteen. The marriage proved a complete success; it was followed by twenty-nine years of almost uninterrupted happiness, and by the birth of fifteen children who included Joseph Justus Scaliger.

A charge of heresy in 1538, of which he was acquitted by his friendly judges, one of whom was his friend Arnoul Le Ferron, was almost the only event of interest during these years, except the publication of his books, and the quarrels and criticisms to which they gave rise. In 1531 he printed his first oration against Erasmus, in defence of Cicero and the Ciceronians. It is a piece of vigorous invective, displaying, like all his subsequent writings, an astonishing command of Latin, and much brilliant rhetoric, but full of vulgar abuse, and completely missing the point of the Ciceronianus of Erasmus.

The writer's indignation at finding it treated with silent contempt by the great scholar, who thought it was the work of a personal enemy - Meander - caused him to write a second oration (published in 1536), more violent and abusive, with more self glorification, but with less real merit than the first. The orations were followed by a prodigious quantity of Latin verse, which appeared in successive volumes in 1533, 1534, 1539, 1546 and 1547; of these, a friendly critic, Mark Pattison, is obliged to approve the judgment of Pierre Daniel Huet, who says, "par ses poésies brutes et informes Scaliger a déshonoré le Parnasse"; yet their numerous editions show that they commended themselves not only to his contemporaries, but to succeeding scholars. A brief tract on comic metres (De comicis dimensionibus) and a work De causis linguae Latinae (Lyon, 1540; Geneva, 1580), which was the earliest Latin grammar founded on scientific principles and following a scientific method, were his only other purely literary works published in his lifetime.

His Poetices (Lyons, 1561; Leyden, 1581) appeared after his death. With many paradoxes, with many criticisms which are below contempt, and many indecent displays of personal animosity — especially in his reference to Etienne Dolet, over whose death he gloated with brutal malignity — it yet contains acute criticism based on the Poetics of Aristotle, imperator noster; omnium bonarum artium dictator perpetuus, an influential treatise in the history of literary criticism. Like many of his generation Scaliger prized Virgil above Homer. His praise of the tragedies of Seneca over those of the Greeks influenced both Shakespeare and Pierre Corneille.

It is as a philosopher and a man of science however that Scaliger meant to be judged. Classical studies he regarded as an agreeable relaxation from severer pursuits. Whatever the truth of the first forty years of his life, he had certainly been a close and accurate observer, and had made himself acquainted with many curious and little known phenomena, which he had stored up in a most tenacious memory.

His scientific writings are all in the form of commentaries, and it was not until his seventieth year that (with the exception of a brief tract on the De insomniis of Hippocrates) he felt that any of them were sufficiently complete to be printed. In 1556 he printed his Dialogue on the De plantis attributed to Aristotle, and in 1557 his Exercitationes on Jerome Cardan's, De subtilitate. His other scientific works, commentaries on Theophrastus' De causis plantarum and Aristotle's History of Animals, he left in a more or less unfinished state, and they were not printed until after his death. They are all marked by arrogant dogmatism, violence of language, a constant tendency to self glorification, strangely combined with extensive real knowledge, with acute reasoning, with an observation of facts and details almost unparalleled. But he is only the naturalist of his own time.

That he anticipated in any manner the inductive reasoning of the true scientific method cannot be contended; his botanical studies did not lead him, like his contemporary Konrad von Gesner, to any idea of a natural system of classification, and he rejected with the utmost arrogance and violence of language the discoveries of Copernicus. In metaphysics and in natural history Aristotle remained as much a law to him as in poetics, and in medicine Galen, but he was not a slave to the text or the details of either. He thoroughly mastered their principles, and is able to see when his masters are not true to themselves. He corrects Aristotle by himself.

He is in that stage of learning when the attempt is made to harmonize the written word with the actual facts of nature, and the result is that his scientific works have only historical value. His Exercitationes upon the De subtilitate of Cardan (1551) is the book by which Scaliger is best known as a philosopher. Its numerous editions bear witness to its popularity, and until the final fall of Aristotle's physics it continued a popular textbook. The Exercitationes are renowned for their display of encyclopaedic wealth of knowledge, the vigour of the author's style, and the accuracy of his observations; at the same time, as Gabriel Naudé noted, they contain more faults than those Scaliger has discovered in Cardan. Charles Nisard wrote also that his object seems to be to deny all that Cardan affirms and to affirm all that Cardan denies. Yet Leibniz and Sir William Hamilton recognize him as the best modern exponent of the physics and metaphysics of Aristotle.

Scaliger died at Agen in 1558.