A growing body of evidence suggests that meditation-based mental practices cause desirable changes to the psychological status. Little is known how enduring changes to multiple aspects of emotions are observed for Japanese long-term practitioners. The present study using a cross-sectional design investigated mindfulness and relevant psychological functions in a population of Japanese yoga practitioners, who routinely practiced classical hatha yoga, breathing techniques, as well as focused attention-based meditation. Training period ranged from 0.3 to 34.0 years. Participants completed a battery of five established Japanese versions of questionnaires, each of which concerned mindfulness, subjective well-being, depression, positive/negative affect, and empathy. Compared with age- and sex-matched control participants, yoga practitioners self-reported significantly higher scores on mindfulness, well-being, positive affect, and empathy, and lower scores on depression and negative affect. Among the practitioners, period and amount of yoga/meditation practice, regardless of ages, predicted higher scores on mindfulness and well-being and lower scores on depression, negative affect, and empathy. These data overall suggest desirable psychological status associated with continued yoga practice among Japanese contemplatives. Implications for comparisons with different cultures and with other traditional practices are discussed.