In May 1960 he graduated from the military college in Omdurman and was commissioned as a second lieutenant in the Sudanese Army and was posted to Shendi with the 10th Brigade, Northern Command.

[5] Among Joseph Lagu's junior officers in Anyanya was John Garang who was recruited in October 1970 and was later to become the chief architect of the second civil war.

In 1985 when Nimeiry's government was toppled by his defence minister, Gen. Mohammed Ahmed Suar-El-Dahab, Joseph Lagu also lost his position as 2nd Vice President.

Al Mahdi's government was in turn overthrown by Gen. Omar al-Bashir (then a Brigadier) who maintained his hold on power until the 2019 Sudanese coup d'état.

[7] He resigned from the position in May 1998 after he was appointment as Presidential Advisor, a post that he declined requesting he be relieved of all official duty so as to become a private citizen and an independent voice.