T follicular helper (Tfh) cells provide critical help to B cells during the germinal centre (GC) reaction by providing cognate interactions that facilitate somatic hypermutation and immunoglobulin class switching necessary for the generation of protective humoral immunity. However, accessing the human lymph node (LN) to capture GC Tfh cell dynamics during in vivo vaccine responses is difficult. Here, we used ultra-sound guided fine needle biopsy to longitudinally sample axillary LNs following seasonal influenza vaccination in healthy human subjects. We show specific expansion of GC cell subsets, including GC Tfh cells and GC B cells, occurs exclusively within draining LNs five days post vaccination. Draining LN GC Tfh and precursor Tfh cells express higher levels of CD38, ICOS and Ki67, indicating that they were significantly more activated, motile and proliferating, compared to contralateral LN cells. Changes in GC Tfh cell populations were paralleled by GC B cells with a significant correlation between these subsets in draining LNs post vaccination. In contrast, there were no changes in the contralateral LNs. These observations provide insight into human Tfh and B cell dynamics within LNs during a vaccine induced memory response and highlights interrogation of critical cellular interactions within lymphoid tissue is essential in understanding early immune responses, that may not be observed in the periphery.