Further to the Catalytic Research Projects, the Working Groups for Academic Collaboration programme involves collectives of researchers whose cooperation is geared towards specified objectives. These collectives can be interdisciplinary and domain-specific groups that focus on specific areas of research, teaching and learning in the HSS field. Working Groups projects can also focus their activities on establishing networks, fostering dialogue, and accelerating the production of research outputs.

The Working Groups programme is intended to give effect to the recommendations in the Charter for the Humanities and Social Sciences on the HSS entity that will fundamentally change the existing higher education landscape to make it more responsive to, and inclusive of, the HSS and its disciplinary particularities. These Working Groups are also aimed at ensuring the integrity and excellence of the HSS in South African higher education institutions. 

The collaboration with academic or university based publishers such as Wits University Press, UKZN Press and the HSRC Press has been successful and several HSS books have been published through this initiative.