In 192, with help from the general Lü Bu and others, he plotted a successful coup in Chang'an against Dong Zhuo, a tyrannical warlord and regent who controlled the Han central government, and assassinated him.

In the 14th-century historical novel Romance of the Three Kingdoms, Wang Yun was the adoptive father of the fictional maiden Diaochan, whom he used to stir up conflict between Lü Bu and Dong Zhuo, causing the former to betray and assassinate the latter.

After the death of Emperor Ling, the general He Jin came into power, and Wang Yun was promoted to the Gentleman of the Household and later to the Intendant of Henan (河南尹).

In 190, the capital Luoyang fell into chaos following the death of He Jin and a bloody clash between the powerful Ten Attendants and government officials.

Dong Zhuo, a warlord from Liang Province (凉州) managed to take control of the situation and eventually placed in the throne a puppet emperor whom he held in his power.

At the time, Wang Yun held the positions of the Minister over the Masses (司徒), replacing Yang Biao,[3] and the Prefect of the Masters of Writing (尚書令).

The plan received a huge boost when the conspirators managed to recruit the help of Lü Bu, a formidable warrior serving as a general under Dong Zhuo.

When Wang Yun refused to grant amnesty to Dong Zhuo's former subordinates, they took up arms under the leadership of Li Jue and Guo Si, who led them to attack Chang'an.

Later in Chapter 9, when Chang'an was surrounded by Li Jue and Guo Si's forces, Wang Yun made them promise to not harm Emperor Xian and then committed suicide in front of them by jumping off the viewing platform above the city gates.