In 1970, Gu joined the Department of Engineering Physics at Tsinghua University. He became an associate professor at its related department, the Department of Physics, in 1985. During his time as an associate professor, he worked as a senior visiting scholar at the University of Notre Dame from 1986 to 1987. After returning to Tsinghua University, he became a full professor in 1988. From 1993 to 1994, he taught as a guest professor at Tohoku University, before returning to Tsinghua University in 1994 to become the chairman of their Department of Physics. Gu became the assistant president and dean of the Tsinghua University graduate school in 2000, and was offered the vice president position in 2001, which he accepted. In 2003, he became the president of Tsinghua University, holding the position for nine years. In 2012, he stepped down from the president position, and became the director of Tsinghua University's Institute for Advanced Study.