It is well established that regular physical exercise enhances memory functions, synaptic plasticity in the hippocampus, and BDNF (Brain Derived Neurotrophic Factor) levels. Likewise, acute exercise benefits hippocampal plasticity in rodents, via increased endocannabinoids (especially anandamide, AEA) and BDNF release. Yet, whether acute exercise affects BDNF and AEA levels and influences memory performance in humans, remains to date unknown. Here we combined blood biomarkers, behavioral, and fMRI measurements to assess the impact of acute physical exercise on associative memory and underlying neurophysiological mechanisms. For each participant, memory was tested after three conditions: rest, moderate or high intensity exercise. A long-term memory retest took place 3 months later. At both test and retest, memory performance after moderate intensity exercise was increased compared to rest and high intensity exercise. We also show that memory after moderate intensity exercise benefited from exercise-induced increases in both AEA and BNDF levels: while AEA boosted hippocampal activity during memory recall, BDNF enhanced hippocampal memory representations and long-term performance. These findings confirm previous results on the benefits of acute exercise towards memory consolidation and, by including the contribution of key biomarkers, extend them by explaining neural plasticity mechanisms mediating cognitive enhancement.