Focused attention meditation (FAM) is a basic meditation practice that cultivates attentional control and monitoring skills. Cross-sectional studies have highlighted high cognitive performance and discriminative neural activity in experienced meditators. However, a direct relationship between neural activity changes and improvement of attention caused by meditation training remains to be elucidated. To investigate this, we conducted a longitudinal study, which evaluated the results of electroencephalography (EEG) during three-stimulus oddball task, resting state, and FAM before and after 8 weeks of FAM training in non-meditators. The FAM training group (n = 17) showed significantly higher P3 amplitude during the oddball task and shorter reaction time for target stimuli compared to that of the control group (n = 20). Furthermore, a significant negative correlation between F4-Oz theta band phase synchrony index (PSI) during FAM and P3 amplitude during the oddball task, and a significant positive correlation between F4-Pz theta band PSI during FAM and P3 amplitude during the oddball task were observed. In contrast, these correlations were not observed in the control group. These findings provide direct evidence of the effectiveness of FAM training and contribute to our understanding of the mechanisms underpinning the effects of meditation on brain activity and cognitive performance.