Possibly born into a Christian family, nothing is known of his early life. Philoponus studied at the school of
Alexandria and began publishing from about 510. He was a pupil and sometime
amanuensis to the Neoplatonic philosopher
Ammonius Hermiae, who had studied at Athens under
Philoponus' early writings are based on lectures given by Ammonius, but gradually he established his own independent thinking in his commentaries and critiques of
On the Soul and
Physics. In the latter work Philoponus became one of the earliest thinkers to reject Aristotle's dynamics and propose the "
theory of impetus":
 i.e., an object moves and continues to move because of an energy imparted in it by the mover and ceases the movement when that energy is exhausted. This insightful theory was the first step towards the concept of
inertia in modern physics, although Philoponus' theory was largely ignored at the time because he was too radical in his rejection of Aristotle.
But this [view of Aristotle] is completely erroneous, and our view may be completely corroborated by actual observation more effectively than by any sort of verbal argument. For if you let fall from the same height two weights, one many times heavier than the other you will see that the ratio of the times required for the motion does not depend [solely] on the weights, but that the difference in time is very small. ... — John Philoponus' refutation of the Aristotelian claim that the elapsed time for a falling body is inversely proportional to its weight
Philoponus is the only writer of antiquity where such a concept is formally presented. As the discovery of the principle of inertia is the hallmark achievement of modern science as it emerges in the 16th to 17th centuries,
Pierre Duhem argues that its invention would put Philoponus among the "great geniuses of Antiquity" and the "principal precursors to modern science", although he holds it more likely that Philoponus may have received the idea from an earlier, otherwise unrecorded
Alexandrian school of mechanics.
In 529 Philoponus wrote his critique
On the Eternity of the World Against Proclus in which he systematically defeats every argument put forward for the
eternity of the world, a theory which formed the basis of pagan attack of the Christian doctrine of
Creation. The intellectual battle against eternalism became one of Philoponus' major preoccupations and dominated several of his publications (some now lost) over the following decade.
He introduced a new period of scientific thought based heavily on three premises: (1) The universe is a product of one single God, (2) the heavens and the earth have the same
physical properties, (3) and the stars are not divine.
 With these principles Philoponus went after his rival,
Simplicius of Cilicia, by questioning Aristotle's' view of dynamics and cosmology.
 He argued that motion can occur in a void and that the velocity of a falling object is not based on its weight.
 He also held that God created all matter with its physical properties and with natural laws that would allow matter to progress from a state of chaos to an organized state forming the present universe.
 What remains of his writings indicate that he used the same
didactic methods of reasoning that modern science uses and that he performed genuine experiments.
The style of his commentaries and his conclusions made Philoponus unpopular with his colleagues and fellow philosophers, and he appears to have ceased his study of philosophy around 530, devoting himself to theology instead. Around 550 he wrote a theological work
On the Creation of the World as a commentary on the
Bible’s story of creation using the insights of Greek philosophers and
Basil the Great. In this work he transfers his theory of impetus to the motion of the planets, whereas Aristotle had proposed different explanations for the motion of heavenly bodies and for earthly projectiles. Thus Philoponus' theological work is recognized in the history of science as the first attempt at a unified theory of dynamics. Another of his major theological concerns was to argue that all material objects were brought into being by God (Arbiter, 52A–B).
Around 553 Philoponus made some theological contributions to the
Council of Constantinople concerning
Christology. His doctrine on Christ's duality, according to which in Christ remain two united substances, united but divided, is analogous to the union of the soul and body in human beings and coincides with the
miaphysite school of thought. He also produced writings on the Trinity around this time. Arbiter, John Philoponus' Christological “opus magnum” stands in the line with
St. Cyril of Alexandria and
Severus of Antioch.
 Philoponus asserted the understanding of Christ as a divine and a human, in opposition to
Chalcedonian authors who strove to reach a middle ground.