Treatment programs based on a neurophysiological model have shown a positive effect on anxiety and depression in tinnitus patients. The aim of this paper was to assess the long-term effect of tinnitus habituation therapy. Sixty-eight individuals were treated with a comprehensive therapy program. The degree of anxiety and depression was assessed before, after, and five years after intervention using the Hospital Anxiety and Depression Scale. The positive and significant changes achieved after habituation therapy (pre = 1.10, post = 0.92 for anxiety and pre = 0.77, post = 0.62 for depression) were maintained five years after treatment ended (0.87 for anxiety and 0.52 for depression). A regression analysis revealed that individual evaluation of the treatment lectures, self-reported health condition, individual experiences of hyperacusis, and hearing loss could explain 44.3% of the variation in anxiety and 30.5% of the variation in depression posttreatment. Five years after, individual evaluation of the treatment lectures and self-reported health condition explained 22.2% of the variation in anxiety. These factors and individual experiences of hyperacusis could further explain 34.9% of the variation in depression. The effect of a neurophysiologic-based management treatment was maintained five years after treatment ended, indicating that the patients continued the improvement process without becoming dependent on professionals.