The main root of the current Zhejiang University, Qiushi Academy, was founded in 1897 and was one of the earliest modern academies of higher education in China. Since 1901, Qiushi Academy had its name changed several times, and even was once suspended. In 1927, on the historic site of the academy, the Third National Sun Yat-sen University was established. On April 1, 1928, it was renamed Chekiang University. Since July 1, 1928, it had been known as National Chekiang University with three schools, namely School of Engineering, School of Agriculture and School of Liberal Arts and Science.

Since the outbreak of the War of Resistance Against Japan, the University was forced to move to Guizhou. Under the guidance of President Chu Kochen, the famous meteorologist, geologist and educator, the University went all the way through difficulties and adversities to establish itself as one of the leading universities in China. It was even honored as "Cambridge of the East" by famous British scholar Joseph Needham. In 1946 the University moved back to Hangzhou. In two years' time, it become a comprehensive university with seven schools, 25 departments, nine research institutes and one research center covering Liberal Arts, Science, Engineering, Agriculture, Normal Education, Law, Medicine and so on.

In 1952, universities in China underwent a nationwide reshuffling due to which the disciplines and institutes of the University were restructured and dissociated. Some institutes were upgraded to become colleges or universities and some merged with other universities such as Hangchow University and Zhejiang Provincial College of Medicine.

Part of the School of Liberal Arts and School of Science merged with School of Liberal Arts and Science of Hangchow University and Zhejiang Education College to form Zhejiang Teacher’s College. In 1958 it was merged to the newly founded Hangzhou University. The School of Agriculture became Zhejiang College of Agriculture, renamed as Zhejiang Agricultural University in 1960. The School of Medicine was merged to Zhejiang Provincial College of Medicine to form Zhejiang Medical College which was later renamed Zhejiang Medical University. After the readjustment and restructuring, Zhejiang University became a multidisciplinary polytechnic university.

The four universities with the same ancestor, Zhejiang University, Hangzhou University, Zhejiang Agricultural University and Zhejiang Medical University, all attained considerable achievements. Zhejiang University became a key national university covering a wide range of disciplines with focuses on engineering. The other three universities, with enormous potential and distinct features, also thrived in respective disciplines. These four universities made remarkable contributions to the development of Zhejiang Province and the whole nation.

With the approval of the State Council, on September 15, 1998, Zhejiang University, Hangzhou University, Zhejiang Agricultural University and Zhejiang Medical University amalgamated into the new Zhejiang University. The new Zhejiang University is oriented toward a comprehensive university with extensive academic capacity and cutting-edge competitiveness, and its founding has been a significant move in the reform and development of China's higher education. Now Zhejiang University is under the direct administration of China's Ministry of Education, with joint support from both the Ministry of Education and Zhejiang Provincial Government.