Following her graduation, Tu Youyou joined the China Academy of Traditional Chinese Medical Sciences (now the China Academy of Chinese Medical Sciences) in Beijing. She remained affiliated with the academy throughout her career, conducting research and mentoring younger scientists.

While best known for her work on artemisinin, Tu Youyou also conducted extensive research on other aspects of traditional Chinese medicine, exploring its potential for treating various diseases. She was a strong advocate for the scientific investigation and validation of traditional remedies.

Tu Youyou rose through the ranks at the China Academy of Chinese Medical Sciences, eventually becoming a senior researcher and chief scientist. She led research teams and mentored numerous students and junior colleagues.