<p>This paper investigates the neural mechanisms underlying the early phase of motor learning in laparoscopic surgery training, using electroencephalography (EEG), brain-derived neurotrophic factor (BDNF) concentrations and subjective cognitive load recorded from <i>n</i> = 31 novice participants during laparoscopy training. Functional connectivity was quantified using inter-site phase clustering (ISPC) and subjective cognitive load was assessed using NASA-TLX scores. The study identified frequency-dependent connectivity patterns correlated with motor learning and BDNF expression. Gains in performance were associated with beta connectivity, particularly within prefrontal cortex and between visual and frontal areas, during task execution (<i>r</i> = − 0.73), and were predicted by delta connectivity during the initial rest episode (<i>r</i> = 0.83). The study also found correlations between connectivity and BDNF, with distinct topographic patterns emphasizing left temporal and visuo-frontal links. By highlighting the shifts in functional connectivity during early motor learning associated with learning, and linking them to brain plasticity mediated by BDNF, the multimodal findings could inform the development of more effective training methods and tailored interventions involving practice and feedback.</p>