The thalamus is an evolutionarily conserved structure with extensive reciprocal connections to cortical regions. While its role in transmitting sensory signals is well-studied, its broader engagement in cognition is unclear. In this review, we discuss evidence that the thalamus regulates functional connectivity within and between cortical regions, determining how a cognitive process is implemented across distributed cortical microcircuits. Within this framework, thalamic circuits do not necessarily determine the categorical content of a cognitive process (e.g., sensory details in feature-based attention), but rather provide a route by which task-relevant cortical representations are sustained and coordinated. Additionally, thalamic control of cortical connectivity bridges general arousal to the specific processing of categorical content, providing an intermediate level of cognitive and circuit description that will facilitate mapping neural computations onto thought and behavior.