Neither of Kepler's parents were interested enough in their oldest son or his future to invest much effort into his education. Fortunately, the region of Germany in which Kepler lived was known for its strong educational system. The schools encouraged students from all economic classes and offered scholarships to those who could not afford tuition. Kepler was launched into academics at an early age.

In elementary school, Kepler learned Latin, which was then considered to be the only language fit for scholarly writing. Due to his frequent illnesses and his family's wanderings, Kepler was unable to attend school consistently – it took him twice as long to finish elementary school as it took the other children. When he was thirteen years old, he entered a theological seminary. There he studied Greek, Latin, theology, rhetoric, music, and math.

According to his own reminiscences, Kepler was a weak, odd, unlikable student who often got bullied and beat up by his peers. But Kepler's enemies were no harsher on him than he was on himself. In his later self-analysis, written in third person, Kepler noted the "dog-like nature" of both his appearance and personality, and added that "morally he was the worst among his contemporaries."

From the theological seminary, Kepler went on to the renowned University of Tuebingen, where he decided to continue his religious studies. He got perfect grades – as did almost every other student at the school. He was successful in his math and physics classes, but decided to devote his life to God.

Before he could earn his graduate degree in divinity, Kepler recieved an unexpected job offer. A Protestant school in the Austrian city of Gratz was in need of a new math professor – and the University of Tuebingen recommended Kepler. Kepler was at first reluctant to accept the job, primarily because he didn't think he was cut out to be an astronomer. He eventually accepted, on the condition that he would be allowed to return to Tuebingen to complete his divinity studies when he wanted to. Tuebingen agreed, but Kepler never returned. He was an astronomer for life.

Kepler arrived in Gratz in April 1594, where he was officially appointed the Mathematicus of the Province. He didn't expect to be a particularly good teacher. From the start, few wanted to take his class, by his second year of teaching, he had no students.

Kepler was initially miserable in Gratz. The town was much smaller and more provincial than he was used to, he was often sick, and as a Protestant, he was constantly on the defense against an oppressive Catholic regime. He was also convinced that the school authorities hated him, and often begged his old associates at Tuebingen to find him a job closer to home. When they were unable to do so, Kepler was forced to remain in Gratz and, contrary to what he believed, the school authorities were happy to keep him there. They expected great things from the young astronomer.

On the rare occasion that Kepler did find himself in front of a class full of students, he distinguished himself from other astronomers of the time. Kepler was one of the only astronomers of the time willing – and in this case – eager to teach the heliocentric system of the universe, which put the sun rather than the earth at its center.

For almost two thousand years, all of Europe had relied upon an intricate vision of the universe created in the second century A.D by the astronomer Ptolemy. Ptolemy's geocentric system places Earth at the center of the universe. This seemed a reasonable enough assumption, since from humanity's point of view, the sun, stars, and planets do seem to revolve around the Earth. Ptolemy argued that the planets and the sun circled the earth in perfectly circular orbits, traveling at constant speeds over time. These two assertions had been the central tenets of astronomical philosophy since the time of Ancient Greece.

However, as it turns out, neither of these two facts are actually true. So in order to make his observations fit his theories, Ptolemy was forced to incorporate a number of imaginary mathematical devices into his system. Each planet's circular orbit around the earth was known as the deferent. But, according to Ptolemy, the planets did not actually travel on the deferent. Instead, they traveled in small orbits around the deferent called epicycles. The system is so intricate that it is difficult to make an accurate count of these wheels-within-wheels, but by Kepler's era, there were somewhere from forty to eighty of them. The final mathematical device required to make reality fit theory was the equant. This was an imaginary point that rotated around the center of the deferent. This was yet another device used to explain why the planets did not appear to be circling the earth with constant, circular motion – when viewed from the equant, the planetary orbits suddenly became circular.

With this type of reasoning, Ptolemy created a universe with an imaginary point for a center. No one believed that such a thing as the equant existed in space – any more than they believed that the planets were actually spinning around on an elaborate system of epicycles. But for centuries, the world was willing to make these mathematical compromises in order to preserve the notion of constant circular motion. Astronomy became a mathematical field divorced from any sense of physical reality. Ptolemy created a geometrically possible system on paper, but steered clear of explaining how the universe actually worked. No one successfully challenged this view for almost two thousand years.