Distinctive patterns of brain neurotransmission frame determinant circuits for behavior. Understanding the relationship between their damage and the cognitive impairment provoked by brain lesions could provide insights into the pathophysiology and therapeutics of disabling disorders, like stroke. Yet, the challenges of neurotransmitter circuits mapping in vivo have hampered this investigation. Here, we developed an MRI white matter atlas of neurotransmitter circuits and created a method to chart how stroke damages neurotransmitter systems, which distinguishes pre and postsynaptic disruption. Our model, trained and tested in two large stroke patient samples, identified eight clusters with different neurochemical patterns. The associations with patients' cognitive profiles were scarce, denoting that a particular cognitive deficit might have finer underlying neurochemical disturbances that are unfit to the granularity of our analyses. These findings depict stroke neurochemical diaschisis patterns, provide insights into stroke cognitive deficits and potential treatments, and open a new window for tailored neurotransmitter modulation.