The university's central administration, foreign student office, and several research institutes are located within the area of the old town, while the new liberal arts campus, with its modern library, overlooks the city from the east.

The university was founded as the "High School of Würzburg" on an initiative started in 1401 by Prince Bishop Johann von Egloffstein.

He wanted to transform the "Gymnasium herbipolense" into a university with four faculties hoping that an influx of teaching staff and students in his territory would cover the need for qualified lawyers and clerics and thus lead to an upturn in the city's economy.

Due to problems with the clergy and administration, however, he was unable to realize his plans After classes had been resumed in some of the subjects in 1551 and the first doctorates had already been awarded in 1567, the Würzburg Prince-Bishop Julius Echter von Mespelbrunn, during the Counter-Reformation, in 1575, first obtained the imperial and then, in 1576, the papal privileges to re-establish the university[12] (see also Erasmus Neustetter called Stürmer).

In 1591, the four-winged university building and the associated church (Neubaukirche) in one of its angles, both commissioned by Julius Echter, were completed.

In 1734, Prince Bishop Friedrich Karl von Schönborn issued new study regulations which opened it up to non-Catholics, too.

But in 1773, the Würzburg Jesuit College was dissolved, and Adam Friedrich von Seinsheim hired followers of the Enlightenment for the theological faculty and thus laid the foundation for its future orientation.

In 1796, the physician and court medicus Anton Müller (1755–1827) began working at Juliusspital in Würzburg; although he never belonged to the university, he became the first psychiatrist in the hospital and the first to publish on his specialty.

Franz Heinrich Meinolf Wilhelm, who as a professor held lectures in German for the first time from 1785, was the first to practice experimental chemistry at the University of Würzburg.

Numerous new buildings were created: for medicine in the vicinity of Juliusspital and Pleicherwall, for the natural sciences on today's Röntgenring and on Koellikerstraße, for dentistry at Pleichertor (demolished in 1879), and for the mental hospital on Schalksberg.

In 1857, the doctor, who had been teaching ophthalmology and dentistry in Würzburg since 1850, opened a private eye clinic in the former birthing house of Adam Elias von Siebold on Klinikstraße 6.

The former delivery house, which had been founded in 1805 as the first maternity clinic in Würzburg and a training center for midwives and obstetricians, in 1857, under Friedrich Wilhelm Scanzoni von Lichtenfels, moved to a new building on Klinikstraße 8.

He developed an inhaler and, after testing it on himself and others in the winter of 1846/47, published the first work on it, and thus established modern anesthesiology in Würzburg.

On 28 October 1896, a new main building, called "Neue Universität", was inaugurated on Sanderring (its construction began in 1892); it is still the seat of the university management today.

Between 1901 and 1911, five Würzburg researchers, whose appointment was mainly due to the mathematician Friedrich Prym (dean and rector), were awarded Nobel Prizes.

After the November Revolution of 1918/19, which ended monarchy in Bavaria, the university also lost its title "Königlich Bayerisch" and was given its current name: "Julius-Maximilians-Universität".

The medical faculty separated from Juliusspital and in 1921 moved to the new University Hospital of Würzburg on the outskirts of the city.

In 1934, under its director Carl Joseph Gauss, the university women's clinic and the affiliated midwifery school moved from Welzhaus on Klinikstraße to the Grombühl district.

According to a report by rector Josef Martin (philologist), the military government had dismissed 123 of the 150 professors who had worked before 1945 and only allowed 27 back to lecture at the university.

The 111-hectare (270-acre) site had been acquired by the Free State of Bavaria from the city of Würzburg in 1962 already, to make room for the more than 6,000 students enrolled at Alma Julia.

Furthermore, on 16 June 1969, the first Bavarian chair for anesthesiology was established in the medical faculty, headed by his professor Karl-Heinz Weis (* 1927).

The drinks, which were mixed with thallium(I) sulfate, were put in front of a lecture hall together with a note declaring them as leftovers from a carnival party and donating them to the freshmen.

The student representatives criticized that the university ran the risk of becoming dependent on its sponsors because the State was reluctant to renovate lecture halls.

[20] The award was given for the removal of structural barriers, especially in new buildings, and for the establishment of the Information Center for People with Disabilities and Chronic Diseases (KIS), created in 2008.

On 7 January 2019, the online portal WueStudy of the University of Würzburg was launched after a lengthy planning and processing phase.