Edmond Halley petitioned and entered Queen's College at Oxford in 1673, at the young age of seventeen.  He was already an expert astronomer with a fine collection of instruments purchased for him by his father.  In 1675, Halley began working with Flamsteed, the Astronomer Royal, by assisting him with observations both at Oxford and at Greenwich.  Flamsteed, was so taken by Halley's knowledge and perseverance, that he wrote in a paper of 1675 and published in the Philosophical Transactions of the Royal Society, Flamsteed remarked: Edmond Halley, a talented young man of Oxford, was present at these observations and assisted carefully with many of them.  Halley made important observations at Oxford, including the August 21, 1676 occultation of Mars by the Moon, which he published in the Philosophical Transactions of the Royal Society.  In November of 1676, Halley gave up on his studies and sailed to St Helena in the southern hemisphere.  Nobody actually knows why he did this, but the most logical explanation may lie in the fact that with the opening of the Royal Observatory at Greenwich in 1675, Flamsteed took on the daunting task of mapping the northern hemisphere stars, so Halley, taking his lead decided to complement this program with the similar task of mapping the stars of the southern hemisphere.  This task required vast amounts of money, Halley obtained the needed financial support not only from his father, but from King Charles II who provided a letter asking the East India Company to take Halley and a colleague to St Helena (the southern-most territory under British rule).  Many other important men also supported Halley's venture, including Brouncker who was president of the Royal Society and Jonas Moore who had been a major influence in the founding of the Royal Observatory.

     The weather in St Helena made astronomical observations difficult at best and had much to be desired.  Despite this Halley's eighteen month stay on the island resulted in his cataloguing of 341 southern hemisphere stars as well as the discovery of a star cluster in Centaurus.  During the voyage Halley improved the sextant, an instrument used for navigation, he collected data relative to the ocean and atmosphere, he noted the equatorial retardation of the pendulum, and made on St Helena, on November 7, 1677, the first complete observation of a transit of Mercury.  He proposed using transits of Mercury or Venus to better determine the distance of the Sun and therefore the scale of the solar system using Kepler's third law of planetary motion.

     In 1678, Halley returned to England and published his catalogue of southern hemisphere stars.  Despite not being an Oxford graduate, Halley still found he had built himself the reputation of one of the leading astronomers of the time.  Honors quickly came his way and he became a graduate of the University of Oxford on December 3, 1678 without taking any degree examinations, the degree was being conferred on Edmond Halley on the command of King Charles II. He was also elected as a member of the Royal Society on November 30, 1678, thus at the age of 22 becoming, one of its youngest Fellows ever.  In 1679 the Royal Society had sent Edmond Halley to Danzig to arbitrate a dispute between Hooke and Hevelius.  Hooke claimed that Hevelius's observations, made without the use of a telescope, could not possibly be accurate.  The 68 year old Hevelius must have been somewhat dismayed to find that a 23 year old man had been sent to judge him.  However, Halley who was a man of great natural diplomacy spent a two months checking the observations of Hevelius, and declared his observations to be accurate.  The fame and recognition which Halley achieved so quickly made for ill will between him and Flamsteed, despite his praise for Halley in his student days.  Flamsteed soon turned against Halley.  Having the Astronomer Royal as an enemy is not the best recommendation for the young astronomer, even one as famous as Halley, and he soon paid the price.

     In 1680 he set out on a European tour with a school friend, Robert Nelson.  Halley had observed a comet while near Calais and travelled on to Paris where, together with Cassini, he made further observations in an attempt to determine its orbit.  Much of 1681 Halley spent back in Italy.  Edmond Halley returned to England in the following year where he married Mary Tooke.  The marriage brought on financial responsibilities to Halley, and his father's recent marriage turned out to be total disaster.  The young Halley had to face the consequence that his support from his father would soon dry up.  More problems soon followed.  In March of 1684 his father vanished without a trace only to be found some five weeks later dead.  As a result of his father's death, Halley found himself administer to his father's personal estate.

     Halley had been involved in an exciting piece of research prior to his father's disappearance.  He had shown that Kepler's third law implied the inverse square law of attraction and presented the results at a meeting of the Royal Society on January 24, 1684.  Halley along with Hooke and Wren, discussed the possibility whether the inverse square law implies elliptical orbits for the planets, but they failed to come up with a proof.  Halley's work on these problems was disrupted for weeks by the difficulties surrounding his father's disappearance and death.  By August of 1682 Halley was pursuing the problem further by visiting Isaac Newton in Cambridge.  He had discovered that Newton had already achieved a proof for the problem along with other highly significant results but did not seem willing to have these results published.

     In 1691, Halley had applied for the vacant Savilian Chair of Astronomy at Oxford.  Given his outstanding research in astronomy, one would have expected him to be appointed to this chair but Flamsteed objected strongly to Halley's appointment to the position.  Flamsteed did not care much for Newton particularly since he felt that Newton had not given sufficient credit to observations made by the Royal Observatory in his theory of the moon.  Thus, Halley's close association with Newton lowered him still further in Flamsteed's eyes.  However, the argument that Flamsteed used against Halley was one which he undoubtedly believed in sincerely, writing to Oxford he believed that Halley would corrupt the youth of the university.  Oxford eventually appointed David Gregory to the chair.