Nan Yang Public School was the embryo of Shanghai Jiao Tong University established in 1896. It was upgraded to Nan Yang College in 1911 and Government Institute of Technology of the Communications Ministry a year later. From 1928 to 1942, it was called the National Chiao Tung University (the Main Campus was in Shanghai). During the Anti-Japanese War (1937 - 1945) the University had been moved to Chongqing, named the National Chiao Tung University, Chongqing Main Campus. This name was used until 1946.

On May 27, 1949, the People's Liberation Army liberated Shanghai City and took over Chiao Tung University on June 15. Some of the professors in the University had moved to Taiwan, they established "National Chiao Tung University" in Hsin Chu County on the island.

Since then, Jiao Tong University had been the name of the campus. From 1959 onwards, it has been divided into two universities, i.e., Shanghai Jiao Tong University and Xi'an Jiao Tong University.

The lost in the First Sino-Japanese War (1894 - 1895) had made China in a deep national crisis. The intellectuals at that time knew to strengthen the power of the nation, the first thing must be done was to cultivate specialists and talents, but for their future career, a good school had to be built ! So in 1896, Mr. Sheng Xuanhuai, a prominent scholar at that time, established Nan Yang Public School in Shanghai. His principle in teaching is "pursuing true knowledge and doing practical things" and aiming to bring up people of talents with good morals.

During 1920s and 30s, Jiao Tong University had been known as one of the best higher educational institutions in China and had a nice nickname, the Oriental MIT. In the heat of the Anti-Japanese War, the University had moved to Chongqing, where professors and lecturers were still hard working, while many patriotic students abandoned their campus life and went to the frontline and died.

Before the founding of new China in 1949, teachers and students took part in the Communists democratic movement. In 1950s, due to the need to conjugate with China's keen desire for economic development, the best faculties of the University gave supports to some brother departments in order to attain faster growth. Later in the 50s, China had been implementing the northwest mass construction project(for safeguarding China’s lifeline), part of the Jiao Tong University's campus moved to northwest China. It became Xi'an Jiao Tong University today. During 1960s and 70s, Shanghai Jiao Tong University had been affiliated to the National Defense Engineering Committee. The University engaged in training of talents in defense science, thus contributed a lot in making the nuclear bomb, missiles and satellites.

Shanghai Jiao Tong University has always been emphasized in cultivating talents in its hundred-year of history, during which it came out more than 200,000 excellent people, including statesmen, scientists, entrepreneurs and engineers, notably the former Chinese President Jiang Zemin, famous scientist Qian Xuesen and many other celebrities in China.

The Reform and Opening Policy has been implemented since the late 1970s. It has an impact on the education field in China, so do Shanghai Jiao Tong University, which has the innovative spirit in engaging academic reforms. The University professors' delegation visited the United States. They introduced the new methods in campus management, received donations from foreign friends and overseas Chinese, so the University's reform was going very smoothly.

In 1984, China's paramount leader, Deng Xiaoping, visited Shanghai Jiao Tong University's leading officials and student representatives. He strongly praised the reform and success that the University had made. Under the supports from Shanghai municipal and state's governments, Shanghai Jiao Tong University resumed and developed many academic subjects, like life sciences, business management and humanities. The University annexed Shanghai Agricultural Academy and Shanghai Second College of Medicine in 1999 and 2005 respectively, thus it has successfully become a comprehensive university and the campus has been expanded too. Meanwhile, Shanghai Jiao Tong University recruited many talents and scientists at home and abroad.

In order to make the University more internationalized, it has cooperated with top academic institutions around the world to provide lectures and distant learning courses.

Now Shanghai Jiao Tong University consists of 21 faculties (with Adult Education, Network Education, Technical School and International Education College). The Secretary of Communist Party Committee of the University is Ma Dexiu and the Chancellor is Zhang Jie. There are full-time undergraduate students about 20,000 and postgraduate students 15,000, with 722 professors, 2256 lecturers and teachers. 33 academicians from China Academy of Sciences and Chinese Academy of Engineering, and 51 guest professors are serving their posts in the University.