In November 1996, Peng disappeared in Kaohsiung, Republic of China; the public last saw her board a yellow Ford Telstar taxi after a DPP meeting the night prior to a DPP convention. She was discovered raped and murdered outside of an abandoned warehouse in Kaohsiung County; her body had more than 30 stab wounds. By 1999 police have received false leads and did not solve the crime.
Peng's murder produced an outcry against a perceived lack of protection given to women in Taiwan. Peng's proposed quota for one fourth of the seats of the elected seats to be reserved for women passed during the November 30, 1996 DPP National Congress meeting; the public believes that Peng died during that day.
The Peng Wan-ru Foundation (彭婉如基金會), an organization established in 1997 which supports women wishing to enter the labour force, was named after Peng.