The appointment follows a recent reshuffle in the ministry of foreign affairs and international cooperation.
The previous deputy minister, Monday Semaya Kumba, was initially dismissed without immediate replacement before subsequently being named as the foreign minister.
This followed the dismissal of Ramadan Goc, who was then appointed as a member of parliament.
Malwal, who served as South Sudan’s permanent representative at the United Nations between 2016 and 2023, now takes the deputy minister role.
Cecilia Adeng had taken over the UN posting in February last year.
Before his UN posting in 2016, Malwal was South Sudan’s ambassador to Ethiopia and Djibouti from 2014.
He at the same time served as permanent representative to the African Union, the Intergovernmental Authority on Development (IGAD), and the United Nations Economic Commission for Africa (UNECA).
From 2012 to 2014, he was the director general of protocol at the foreign affairs ministry in Juba, after having served as the ministry’s director of protocol starting in 2011. He is the son of veteran South Sudanese politician Bona Malwal Madut.