The office of the President of Chongqing University, currently held by Wang Shuxin, was created with the founding of Chongqing University in 1929 as the chief executive officer of the school.
After the founding of the Communist State, each president is appointed by and is responsible to the Central Committee of the Chinese Communist Party and the State Council, who is delegated the day-to-day running of the university. In reality, the university President reports to the Party Secretary in the university's Communist Party committee.
| Period | Year | President (English name) | President (Chinese name) | Alma mater | Ref |
| Chongqing University | October 1929–August 1935 | Sichuan Military College | |||
| Sichuan Provincial Chongqing University | August 1935–July 1938 | ||||
| October 1938–July 1941 | |||||
| National Chongqing University | September 1941–November 1949 | ||||
| Chongqing University | March 1950–November 1952 | He Lu | |||
| July 1956–August 1966 | Zheng Siqun | ||||
| April 1978–May 1980 | Zeng Delin | ||||
| May 1980–April 1982 | He Wenqin | ||||
| December 1982–December 1986 | |||||
| December 1986–August 1992 | Chongqing University Saint Petersburg State Polytechnic University | ||||
| August 1992–August 1996 | Wu Yunpeng | ||||
| August 1996–July 1997 | Liu Fei | ||||
| July 1997–January 2003 | Wu Zhongfu | Chongqing University | |||
| January 2003–December 2010 | Chongqing University | ||||
| December 2010–June 2013 | |||||
| June 2013–present | |||||
| December 2017–April 2022 | Zhang Zongyi | ||||
| June 2022–present | [1] |
| Period | Year | Communist Party Secretary (English name) | Communist Party Secretary (Chinese name) | Alma mater | Ref |
| Chongqing University | December 1953–August 1966 | Zheng Siqun | |||
| April 1972–May 1980 | Zeng Delin | ||||
| May 1980–February 1982 | He Wenqin | ||||
| February 1982–August 1983 | Zhang Wencheng | ||||
| August 1983–May 1989 | Cheng Diquan | ||||
| August 1989–April 1997 | Gu Leguan | Chongqing University Saint Petersburg State Institute of Technology | |||
| April 1997–May 2000 | Ou Keping | Chongqing University | |||
| May 2000–December 2005 | Zhu Jialin | Peking University Pierre and Marie Curie University | |||
| December 2005–October 2015 | Ou Keping | Chongqing University | |||
| October 2015–December 2019 | Zhou Xun | ||||
| January 2020–present | Shu Lichun | Chongqing University |