Devaluation protocols reveal that Tourette patients show an increased propensity to habitual behaviors as they continue to respond to devalued outcomes in a cognitive stimulus-response-outcome association task. We use a neuro-computational model of hierarchically organized cortico-basal ganglia-thalamo-cortical loops to shed more light on habit formation and its alteration in Tourette patients. In our model, habitual behavior emerges from cortico-thalamic shortcut connections, where enhanced habit formation can be linked to faster plasticity in the shortcut or to a stronger feedback from the shortcut to the basal ganglia. We explore two major hypotheses of Tourette pathophysiology—local striatal disinhibition and increased dopaminergic modulation of striatal medium spiny neurons—as causes for altered shortcut activation. Both model changes altered shortcut functioning and resulted in higher rates of responses towards devalued outcomes, similar to what is observed in Tourette patients. We recommend future experimental neuroscientific studies to locate shortcuts between cortico-basal ganglia-thalamo-cortical loops in the human brain and study their potential role in health and disease.