Kepler's early education was in a local school and then at a nearby seminary, from which, intending to be ordained, he went on to enrol at the University of Tubingen, then (as now) a bastion of Lutheran orthodoxy.

At this time, it was usual for all students at a university to attend courses on "mathematics". In principle this included the four mathematical sciences: arithmetic, geometry, astronomy and music. It seems, however, that what was taught depended on the particular university. At Tubingen Kepler was taught astronomy by one of the leading astronomers of the day, Michael Maestlin (1550 - 1631). The astronomy of the curriculum was, of course, geocentric astronomy, that is the current version of the Ptolemaic system, in which all seven planets - Moon, Mercury, Venus, Sun, Mars, Jupiter and Saturn - moved round the Earth, their positions against the fixed stars being calculated by combining circular motions. This system was more or less in accord with current (Aristotelian) notions of physics, though there were certain difficulties, such as whether one might consider as 'uniform' (and therefore acceptable as obviously eternal) a circular motion that was not uniform about its own centre but about another point (called an 'equant'). However, it seems that on the whole astronomers (who saw themselves as 'mathematicians') were content to carry on calculating positions of planets and leave it to natural philosophers to worry about whether the mathematical models corresponded to physical mechanisms. Kepler did not take this attitude. His earliest published work (1596) proposes to consider the actual paths of the planets, not the circles used to construct them.

At Tubingen, Kepler studied not only mathematics but also Greek and Hebrew (both necessary for reading the scriptures in their original languages). Teaching was in Latin. At the end of his first year Kepler got 'A's for everything except mathematics. Probably Maestlin was trying to tell him he could do better, because Kepler was in fact one of the select pupils to whom he chose to teach more advanced astronomy by introducing them to the new, heliocentric cosmological system of Copernicus. It was from Maestlin that Kepler learned that the preface to On the revolutions, explaining that this was 'only mathematics', was not by Copernicus. Kepler seems to have accepted almost instantly that the Copernican system was physically true; his reasons for accepting it will be discussed in connection with his first cosmological model (see below).

It seems that even in Kepler's student days there were indications that his religious beliefs were not entirely in accord with the orthodox Lutheranism current in Tubingen and formulated in the 'Augsburg Confession' (Confessio Augustana). Kepler's problems with this Protestant orthodoxy concerned the supposed relation between matter and 'spirit' (a non-material entity) in the doctrine of the Eucharist. This ties up with Kepler's astronomy to the extent that he apparently found somewhat similar intellectual difficulties in explaining how 'force' from the Sun could affect the planets. In his writings, Kepler is given to laying his opinions on the line - which is very convenient for historians. In real life, it seems likely that a similar tendency to openness led the authorities at Tubingen to entertain well-founded doubts about his religious orthodoxy. These may explain why Maestlin persuaded Kepler to abandon plans for ordination and instead take up a post teaching mathematics in Graz. Religious intolerance sharpened in the following years. Kepler was excommunicated in 1612. This caused him much pain, but despite his (by then) relatively high social standing, as Imperial Mathematician, he never succeeded in getting the ban lifted.

Kepler's years in Prague were relatively peaceful, and scientifically extremely productive. In fact, even when things went badly, he seems never to have allowed external circumstances to prevent him from getting on with his work. Things began to go very badly in late 1611. First, his seven year old son died. Kepler wrote to a friend that this death was particularly hard to bear because the child reminded him so much of himself at that age. Then Kepler's wife died. Then the Emperor Rudolf, whose health was failing, was forced to abdicate in favour of his brother Matthias, who, like Rudolf, was a Catholic but (unlike Rudolf) did not believe in tolerance of Protestants. Kepler had to leave Prague. Before he departed he had his wife's body moved into the son's grave, and wrote a Latin epitaph for them. He and his remaining children moved to Linz (now in Austria).

Kepler seems to have married his first wife, Barbara, for love (though the marriage was arranged through a broker). The second marriage, in 1613, was a matter of practical necessity; he needed someone to look after the children. Kepler's new wife, Susanna, had a crash course in Kepler's character: the dedicatory letter to the resultant book explains that at the wedding celebrations he noticed that the volumes of wine barrels were estimated by means of a rod slipped in diagonally through the bung-hole, and he began to wonder how that could work. The result was a study of the volumes of solids of revolution (New Stereometry of wine barrels ..., Nova stereometria doliorum ..., Linz, 1615) in which Kepler, basing himself on the work of Archimedes, used a resolution into 'indivisibles'. This method was later developed by Bonaventura Cavalieri (c. 1598 - 1647) and is part of the ancestry of the infinitesimal calculus.

Kepler died 15 Nov 1630 in Regensburg(now in Germany), after a short illness. He was staying in the city on his way to collect some money owing to him in connection with the Rudolphine Tables. He was buried in the local church, but this was destroyed in the course of the Thirty Years' War and nothing remains of the tomb.