Psychodynamic conflicts form an important construct to understand the genesis and maintenance of mental disorders. Conflict-related themes should therefore provoke strong reactions on the behavioral, physiological, and neural level. We confronted N = 18 healthy subjects with a vast array of sentences describing typical psychodynamic conflict themes in the fMRI scanner and let them associate spontaneously in reaction. The overt associations were then analyzed according to psychoanalytic theory and the system of operationalized psychodynamic diagnosis and used as a genuinely psychodynamic indicator, whether each potentially conflict-related sentence actually touched a conflict theme of the individual. Behavioral, physiological, and neural reactions were compared between those subjects with an “apparent conflict” and those with “absent conflicts.” The first group reported stronger agreement with the conflict-related sentences, more negative valence in reaction, had higher levels of skin conductance reactivity and exhibited stronger activation in the anterior cingulate cortex, amongst other functions involved in emotion processing and conflict-monitoring. In conjunction, we interpret this activity as a possible correlate of subjects’ inherent reactions and regulatory processes evoked by conflict themes. This study makes a point for the fruitfulness of the neuropsychoanalytic endeavor by using free association, the classical technique most commonly used in psychoanalysis, to investigate aspects of conflict processing in neuroimaging.