In 1976, she was appointed as Legal Officer of the Ministry of Labour and Attorney General's Chambers. She was appointed in January 1979 as Magistrate in Malacca and became president of the Session Court in Johor Bahru in December 1981. 

In the middle to late 1980s, she was Senior Federal Counsel to several Government units, including the Ministry of Defence in November 1985 and the Prime Minister's Department in March 1988.    

She was named Chief Registrar of the Federal Court of Malaysia in November 1994 and Judicial Commissioner of the High Court of Malaya, Kuala Lumpur in August 1996.

She served as High Court Judge in Shah Alam Johor and Kuala Lumpur from 1998 to 2001. In 2006, she was elevated to be Court of Appeal Judge and served until 2012. She was appointed as Federal Court Judge on 4 April 2012.

Tan Sri Datuk Zainun has been appointed to the Advisory Board of the United Nations Global Judiciary Integrity Network in 2018.

At present, Tan Sri Datuk Zainun is a Board Member of Permodalan Nasional Berhad (PNB) and Deputy Chairman of Enforcement Agency Integrity Commission (EAIC).

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