He undertook doctoral studies in palaeoanthropology at the University of the Witwatersrand (Wits) in South Africa under Professor Phillip Tobias, focusing his research on the shoulder girdle of early hominins; he graduated in 1994.

He is presently a research professor in the same topic at the Evolutionary Studies Institute (ESI) and the Centre of Excellence in Palaeosciences (CoE Pal) at Wits.

[18][non-primary source needed][19][20] Scholars have disputed the argument that these individuals are pygmoid in stature, or that they were the result of insular dwarfism;[19][21] in an article titled "Small Scattered Fragments Do Not a Dwarf Make", anthropologists Scott M. Fitzpatrick (NC State), Greg C. Nelson (University of Oregon), and Geoffrey Clark (Australian National University) conclude that "[p]rehistoric Palauan populations were normal-sized and exhibit traits that fall within the normal variation for Homo sapiens," hence, concluding that their evidence did "not support the claims by Berger et al. (2008) that there were smaller-bodied populations living in Palau or that insular dwarfism took place"[22] Berger and co-authors Churchill and De Klerk replied to the study, saying "the logical flaws and misrepresentations in Fitzpatrick and coworker's paper are too numerous to discuss in detail" and that their restudy report "amounts to a vacuous argument from authority... and ad hominem assault, and brings little new data to bear on the question of body size and skeletal morphology in early Palauans".

[23] John Hawks, the paleoanthropologist who edited the original Palau article for PLoS ONE, has replied in part to some of the dissenting researchers' claims (in his personal web blog).

Along with various co-authors, Berger published a series of articles between 2010 and 2013 in the journal Science that describe what they call a new species, Australopithecus sediba, which had a mixture of primitive and modern characteristics.

[28] On September 13, 2013, two recreational cavers, Rick Hunter and Steven Tucker, discovered a previously unknown, remote chamber within the well known Rising Star cave system.

Recognizing their importance, and unable to access the chamber himself due to his size, Berger organized an expedition over social media that brought six qualified researchers in from around the world to commence an excavation of the remains in November 2013.

[33] Berger stated that he and his colleagues had established the existence of intentional burials, the controlled use of fire, and the carving of primitive rock art by Homo naledi in the subchamber.

[34][35] Over the next few weeks, Berger appeared on numerous talk show interviews, podcasts, YouTube channels, and other popular media formats, again stating conclusively that the Homo naledi had engaged in the aforementioned behaviors, despite no peer-reviewed evidence having been made public yet.

The reviews noted myriad issues such as extensive lack of relevant citation and evidence, misleading and prematurely conclusive language, and a widespread pattern of trying to prove a preconceived hypothesis (e.g. intentional burials as opposed to natural deposition) rather than following objective scientific process, with one reviewer describing the paper as "storytelling for a popular news article instead of a scientific paper", and another describing the overall perspective as “HARKing”.

[41][42][43] Six days after the initial 2023 publications in eLife, a documentary about Berger and the Rising Star excavation entitled Unknown: Cave of Bones was released for streaming on Netflix.

[44] On August 8, 2023, Penguin Random House published an autobiographical account about the excavations, written by Berger and University of Wisconsin anthropologist John Hawks.

[45] Collaborative research papers by Berger have been recognized four times as being among the top 100 Science stories of the year by Discover Magazine,[citation needed] an international periodical focusing on popular scientific issues.