Mental rotation is a crucial cognitive skill underlying performance in various spatial tasks. It can be enhanced through repetitive practice in previous studies. However, the long-term efficacy of training and non-invasive brain stimulation and its associated neurophysiological correlates are yet to be elucidated. This study investigated the long-term after-effects of 10 days of mental rotation training with high-definition transcranial direct current stimulation (HD-tDCS) on behavioral performance and neural electrophysiology in 34 healthy participants. Mental rotation tests along with EEG recording were performed 1 day before training, 1 day, 20 days, and 90 days after training. While no significant group differences emerged due to stimulation, training resulted in improved task accuracy, decreased response time, and increased task-evoked EEG responses. These effects diminished over time in the follow-up tests but remained superior to pre-training levels at 90 days. Surprisingly, there was still a sustained elevation in task-evoked neurophysiological responses 20 days after training compared to 1 day after training. Individual differences, such as gender and baseline performance, probably modulated training outcomes and long-term after-effects. These findings shed light on the potential of mental rotation training to enhance cognitive function and highlight the feasibility and necessity for further exploration of training to enhance cognitive-related neuroplasticity.