Follicular CD4+ T helper (Tfh) cells are critical for the generation of humoral immune responses to pathogenic infections, providing help for B cell development, survival, and affinity maturation of antibodies. Although CD4+ Tfh cells are reported to accumulate in HIV or SIV infection, here we found that germinal center (GC) Tfh cells, defined here as CXCR5+PD-1HIGHCD4+ T cells, did not consistently accumulate in chronically SIV-infected rhesus macaques compared with those infected with less pathogenic SHIV, vaccinated and SIVmac-challenged, or SIVmac-infected Mamu-A*01+ macaques, all of which are associated with some control of virus replication and slower disease progression. Interestingly, CXCR5+PD-1HIGH Tfh cells in lymphoid tissues were eventually depleted in macaques with AIDS compared to the other cohorts. Chronic activation and proliferation of CXCR5+PD-1HIGH Tfh were increased, yet PD-L2 expression was downregulated on B cells, possibly resulting in GC Tfh cell apoptosis. Together, these findings suggest changes in CXCR5+PD-1HIGH Tfh cells in lymph nodes correlate with immune control during infection, and their loss or dysregulation contribute to impairment of B cell responses and progression to AIDS.