This study aimed to identify the interrelationships between mature BDNF (mBDNF), precursor BDNF (proBDNF) trajectories, and cognitive performance in individuals with HIV from sub-Saharan Africa over 96 weeks following antiretroviral therapy (ART) initiation. Using data from 154 participants in the ACTG 5199 study (ClinicalTrials.gov NCT00096824, 2005-06-23) in Johannesburg and Harare (2006-2009), we measured serum mBDNF and proBDNF levels via ELISA and assessed cognitive performance with neuropsychological tests. Group-based trajectory modelling indicated two mBDNF trajectories-"Stable Ascent" (83.9%) and "Peak with Gradual Decline" (16.1%)-and two proBDNF trajectories-"Gradual Increase" (85.7%) and "Gradual Decline" (14.3%). These were linked to three cognitive trajectories: "Low Baseline-Slow Improvement," "Gradual Improvement," and "Late Surge." The "Stable Ascent" mBDNF group showed a significant probability of "Gradual Improvement" (68%) in cognitive performance and a "Late Surge" (9.5%). In contrast, the "Peak with Gradual Decline" mBDNF trajectory saw no "Late Surge." A "Gradual Increase" in proBDNF corresponded to a 67.7% chance of "Gradual Improvement" in cognition. Findings suggest BDNF isoforms as potential biomarkers for cognitive interventions in HIV, emphasizing that stable or increasing BDNF levels post-ART are linked to favourable cognitive outcomes. Further research is needed to develop BDNF-based cognitive health strategies to improve outcomes for people with HIV.