HIV-1 integration is required for high levels of viral expression, and constitutes a key therapeutic target. Unintegrated viral DNA (uDNA) can support only limited transcription but may contribute to viral propagation, persistence and/or treatment escape under specific situations. Here, we demonstrate, for the first time, that the expression of HIV uDNA is mainly supported by 1-LTR circles, and regulated in the opposite way, relatively to integrated DNA (iDNA), following NF-B pathway modulation. Upon treatment activating this pathway, NF-B p65 and AP-1 (cFos/cJun) binding to HIV LTR iDNA correlates with increased iDNA expression. On the contrary, inhibition of NF-B pathway promotes the expression of uDNA. Finally, this study opens new insights on the potential roles of episomal genomes during the HIV-1 latency and persistence.