In this study we investigated the effect of musical training and emotional content of stimuli on time estimation. Eighty students aged 12 to 15 years were equally divided into two main groups (musicians, non-musicians) based on whether they had formal music education or not. The participants took part in a music listening task and were asked to estimate the duration of a happy or a sad song. The results showed that: musical training affects temporal perception by allowing individuals to make more accurate estimations of time durations; the emotional content of the song affects time estimation, especially in the case of non-musicians; non-musicians overestimate the duration of sad songs while they underestimate the duration in the case of happy songs. These results emphasize the close relationship between time estimation, musical training, and emotion.